Table S2 QC stats

Table S1 is iPSN differentiation protocols

multiqc_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), 
                                                                                                  # multiqc_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_stat_paths)
                                                                                                  ) %>% pull(multiqc_stat_paths)
multiqc_stats.tsv = multiqc_stat_paths %>% map(read_tsv, show_col_types = FALSE)                                                                        
names(multiqc_stats.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(dataset)
multiqc_data <- map_dfr(multiqc_stats.tsv, bind_rows, .id = "dataset") %>% clean_names() %>% drop_na(samtools_mqc_generalstats_samtools_flagstat_total) %>% filter(sample %in% ipsc_mn_als_datasets_with_lee.metadata$sample) %>%
  mutate(dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincs0" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS", dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~ dataset)) %>%
  select(dataset, sample, raw_total_sequences = samtools_mqc_generalstats_samtools_raw_total_sequences, flagstat_total = samtools_mqc_generalstats_samtools_flagstat_total, mapped_passed = samtools_mqc_generalstats_samtools_mapped_passed, reads_mapped = samtools_mqc_generalstats_samtools_reads_mapped, reads_mapped_percent = samtools_mqc_generalstats_samtools_reads_mapped_percent, reads_aligned = quali_map_mqc_generalstats_qualimap_reads_aligned, r_rna_percent = biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna, bias_5_3 = quali_map_mqc_generalstats_qualimap_5_3_bias, proper_pairs_percent = r_se_qc_mqc_generalstats_rseqc_proper_pairs_percent, reads_assigned_percent = feature_counts_mqc_generalstats_featurecounts_percent_assigned, reads_assigned = feature_counts_mqc_generalstats_featurecounts_assigned, percent_duplication = picard_mqc_generalstats_picard_percent_duplication, error_rate = samtools_mqc_generalstats_samtools_error_rate, non_primary_alignments = samtools_mqc_generalstats_samtools_non_primary_alignments, reads_properly_paired_percent = samtools_mqc_generalstats_samtools_reads_properly_paired_percent, percent_mapped = salmon_mqc_generalstats_salmon_percent_mapped, num_mapped = salmon_mqc_generalstats_salmon_num_mapped, uniquely_mapped_percent = star_mqc_generalstats_star_uniquely_mapped_percent, uniquely_mapped = star_mqc_generalstats_star_uniquely_mapped, percent_trimmed =cutadapt_mqc_generalstats_cutadapt_percent_trimmed, total_sequences = fast_qc_mqc_generalstats_fastqc_total_sequences, raw_percent_gc = fast_qc_raw_mqc_generalstats_fastqc_raw_percent_gc, raw_avg_sequence_length = fast_qc_raw_mqc_generalstats_fastqc_raw_avg_sequence_length, trimmed_percent_duplicates = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_duplicates, trimmed_percent_gc = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_gc)
kbl(multiqc_data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")
dataset sample raw_total_sequences flagstat_total mapped_passed reads_mapped reads_mapped_percent reads_aligned r_rna_percent bias_5_3 proper_pairs_percent reads_assigned_percent reads_assigned percent_duplication error_rate non_primary_alignments reads_properly_paired_percent percent_mapped num_mapped uniquely_mapped_percent uniquely_mapped percent_trimmed total_sequences raw_percent_gc raw_avg_sequence_length trimmed_percent_duplicates trimmed_percent_gc
AnswerALS CASE_NEUAA599TMX 90172968 110049375 110049375 90172968 100 45083935 0.0000341 0.99 67.98135 42.58702 23434669 0.143612 0.0024970 19876407 99.99435 100 24209931 92.84 42383420 NA NA NA NA NA NA
AnswerALS CASE_NEUAB000NKC 89923754 126498124 126498124 89923754 100 44958805 0.0005546 0.98 53.83124 44.75184 28306923 0.209232 0.0027416 36574370 99.99317 100 29638747 89.01 40901591 NA NA NA NA NA NA
AnswerALS CASE_NEUAE228FF6 130825845 271586963 271586963 130825845 100 65399474 0.0007375 0.98 22.06248 22.76193 30915467 0.514356 0.0017731 140761118 99.97944 100 33394237 79.24 53277634 NA NA NA NA NA NA
AnswerALS CASE_NEUAE993EPR 125072312 165724188 165724188 125072312 100 62531785 0.0003629 1.01 54.17946 44.55271 36920158 0.254615 0.0020875 40651876 99.99301 100 39957256 88.95 56894281 NA NA NA NA NA NA
AnswerALS CASE_NEUAF553MJ3 111693376 150525878 150525878 111693376 100 55843369 0.0007157 0.96 59.10802 33.41668 25151814 0.173674 0.0027145 38832502 99.99406 100 26254962 89.88 51139673 NA NA NA NA NA NA
AnswerALS CASE_NEUAG241NUD 128635564 176979996 176979996 128635564 100 64313593 0.0002679 1.00 48.16291 37.53702 33218721 0.312094 0.0020796 48344432 99.99349 100 35528664 88.92 58281646 NA NA NA NA NA NA
AnswerALS CASE_NEUAG603XLK 49130010 65504049 65504049 49130010 100 24563226 0.0000682 0.97 60.69713 40.28262 13194300 0.158176 0.0027302 16374039 99.99276 100 13971295 90.56 22629235 NA NA NA NA NA NA
AnswerALS CASE_NEUAG766ULB 126929964 183940593 183940593 126929964 100 63460674 0.0001364 0.97 44.39181 36.66220 33721322 0.327647 0.0019348 57010629 99.99321 100 38009904 86.00 55851641 NA NA NA NA NA NA
AnswerALS CASE_NEUAL076FCE 131833174 167516336 167516336 131833174 100 65912690 0.0001157 1.00 51.01627 46.44480 38903923 0.328565 0.0020416 35683162 99.99409 100 41680265 90.36 60722395 NA NA NA NA NA NA
AnswerALS CASE_NEUAM655HF7 87433717 136427989 136427989 87433717 100 43714307 0.0007112 0.97 49.04198 35.24584 24043842 0.198245 0.0026647 48994272 99.99416 100 25533781 87.06 38824703 NA NA NA NA NA NA
AnswerALS CASE_NEUAP285GGU 105486258 156711695 156711695 105486258 100 52739534 0.0001533 0.99 43.73658 32.45820 25434619 0.320706 0.0021994 51225437 99.99318 100 27807432 86.72 46727085 NA NA NA NA NA NA
AnswerALS CASE_NEUAT234RK6 120938977 151644990 151644990 120938977 100 60463545 0.0000474 1.01 55.15200 41.70809 31627358 0.283175 0.0020793 30706013 99.99017 100 34225046 89.90 55453618 NA NA NA NA NA NA
AnswerALS CASE_NEUAW157NMJ 114977089 145878754 145878754 114977089 100 57485309 0.0000300 0.98 62.68947 45.63163 33285218 0.176876 0.0026261 30901665 99.99437 100 34142140 92.00 53691857 NA NA NA NA NA NA
AnswerALS CASE_NEUAW717TN6 126834297 159575177 159575177 126834297 100 63405958 0.0000835 1.00 58.45321 34.49994 27532068 0.239585 0.0019821 32740880 99.98235 100 28895482 90.26 58851386 NA NA NA NA NA NA
AnswerALS CASE_NEUAX665ZHY 139537273 231443631 231443631 139537273 100 69763285 0.0002681 0.98 39.84617 29.65286 34317241 0.309280 0.0019313 91906358 99.99233 100 38214892 84.78 60401717 NA NA NA NA NA NA
AnswerALS CASE_NEUAY067UTB 153856323 214267305 214267305 153856323 100 76923947 0.0005954 1.02 46.70964 36.05257 38626623 0.324427 0.0020446 60410982 99.99452 100 41699625 88.96 69716387 NA NA NA NA NA NA
AnswerALS CASE_NEUAZ394JEZ 134436051 178480252 178480252 134436051 100 67210701 0.0001388 1.00 48.50850 37.12241 33133119 0.328293 0.0022132 44044201 99.98910 100 37250812 86.85 60348215 NA NA NA NA NA NA
AnswerALS CASE_NEUBA169GXD 123489072 183039179 183039179 123489072 100 61738330 0.0002351 1.01 47.16187 38.10750 34879845 0.270775 0.0019934 59550107 99.98995 100 37301727 85.89 54952243 NA NA NA NA NA NA
AnswerALS CASE_NEUBC901KL3 128790984 158512044 158512044 128790984 100 64386445 0.0001962 0.99 58.53930 45.65992 36193674 0.253956 0.0019522 29721060 99.98595 100 37879352 91.83 60115760 NA NA NA NA NA NA
AnswerALS CASE_NEUBC998WWB 135317031 201372187 201372187 135317031 100 67654064 0.0005399 0.97 46.27861 33.47649 33708237 0.280293 0.0020378 66055156 99.99342 100 35826821 87.60 60600596 NA NA NA NA NA NA
AnswerALS CASE_NEUBD218YR3 94340954 144759706 144759706 94340954 100 47167578 0.0000192 0.98 48.05228 43.19240 31264298 0.227102 0.0027411 50418752 99.99385 100 34033859 87.16 41925594 NA NA NA NA NA NA
AnswerALS CASE_NEUBD288RXQ 116501755 146458489 146458489 116501755 100 58246918 0.0002148 0.94 60.91542 28.60820 20951015 0.209542 0.0021196 29956734 99.99320 100 21670764 91.97 54377155 NA NA NA NA NA NA
AnswerALS CASE_NEUBK117YXL 124612330 176723226 176723226 124612330 100 62302088 0.0011893 1.00 50.17024 34.82647 30775311 0.258965 0.0021462 52110896 99.99346 100 32249185 88.26 56369904 NA NA NA NA NA NA
AnswerALS CASE_NEUBM949LA5 123889216 181640803 181640803 123889216 100 61938822 0.0003055 1.00 45.47430 36.03590 32731139 0.303790 0.0020690 57751587 99.99066 100 35619732 87.21 55164621 NA NA NA NA NA NA
AnswerALS CASE_NEUBN979ZZ5 121537754 158678819 158678819 121537754 100 60763327 0.0000682 1.01 54.39141 44.35331 35193014 0.260889 0.0018488 37141065 99.99087 100 38577212 89.17 55260530 NA NA NA NA NA NA
AnswerALS CASE_NEUBT273FH3 110747555 139595936 139595936 110747555 100 55368342 0.0002129 1.01 51.51089 49.11158 34282757 0.326915 0.0019341 28848381 99.99018 100 38296907 89.49 50443790 NA NA NA NA NA NA
AnswerALS CASE_NEUBW008RJ5 148445384 191169979 191169979 148445384 100 74215056 0.0000695 1.00 53.75423 42.16076 40303598 0.281581 0.0020311 42724595 99.98971 100 43213983 90.70 68428153 NA NA NA NA NA NA
AnswerALS CASE_NEUBY734PFR 89534532 117260923 117260923 89534532 100 44764400 0.0002683 0.96 61.13324 42.59420 24974733 0.168385 0.0027772 27726391 99.99360 100 26194066 90.53 41347426 NA NA NA NA NA NA
AnswerALS CASE_NEUCB613CA9 120314012 157070980 157070980 120314012 100 60153084 0.0001226 0.98 55.67521 38.41598 30172303 0.247442 0.0019572 36756968 99.99348 100 32529148 89.89 55041136 NA NA NA NA NA NA
AnswerALS CASE_NEUCD502BFU 122416921 163718351 163718351 122416921 100 61200013 0.0002703 0.98 52.61787 44.28361 36255523 0.268173 0.0020632 41301430 99.98620 100 37130970 90.10 56342440 NA NA NA NA NA NA
AnswerALS CASE_NEUCE965ZGK 99739464 146713178 146713178 99739464 100 49866419 0.0000423 0.97 51.30799 41.90401 30741292 0.211673 0.0026514 46973714 99.99336 100 32466869 88.12 44747465 NA NA NA NA NA NA
AnswerALS CASE_NEUCF538BRM 124776812 147487594 147487594 124776812 100 62382563 0.0000829 0.98 64.21820 40.91160 30172840 0.218006 0.0021087 22710782 99.99063 100 31309221 92.23 58712724 NA NA NA NA NA NA
AnswerALS CASE_NEUCG511MJ6 141403477 188997248 188997248 141403477 100 70694493 0.0001681 0.97 50.33612 39.01470 36872585 0.301172 0.0022295 47593771 99.98975 100 39203261 88.35 64401376 NA NA NA NA NA NA
AnswerALS CASE_NEUCN596RR3 107638838 136547448 136547448 107638838 100 53815848 0.0002137 0.97 63.39855 39.05644 26667044 0.168394 0.0027305 28908610 99.99336 100 28293153 91.27 49945306 NA NA NA NA NA NA
AnswerALS CASE_NEUCP218XVV 133693665 206523773 206523773 133693665 100 66837184 0.0005851 0.97 43.34389 36.40578 37599113 0.298408 0.0020207 72830108 99.98557 100 39426915 85.76 59265499 NA NA NA NA NA NA
AnswerALS CASE_NEUCT022VTK 139555913 173337477 173337477 139555913 100 69771316 0.0000122 0.96 56.24646 47.25522 40959489 0.277179 0.0020943 33781564 99.99048 100 42662232 91.68 64970108 NA NA NA NA NA NA
AnswerALS CASE_NEUCT842RJV 132288250 170017088 170017088 132288250 100 66141468 0.0000451 0.98 48.80887 49.59928 42165473 0.348855 0.0018535 37728838 99.99598 100 47530437 89.52 60131099 NA NA NA NA NA NA
AnswerALS CASE_NEUCU076ADN 138846225 192907404 192907404 138846225 100 69417377 0.0004188 0.99 47.60645 44.06356 42504669 0.310876 0.0018324 54061179 99.99174 100 45038105 88.31 62770985 NA NA NA NA NA NA
AnswerALS CASE_NEUCU245GBQ 89412399 120947846 120947846 89412399 100 44703436 0.0000910 0.96 57.40010 45.43816 27479901 0.193442 0.0027497 31535447 99.99382 100 29510050 89.99 40911080 NA NA NA NA NA NA
AnswerALS CASE_NEUCV578DFJ 111373277 166478871 166478871 111373277 100 55679121 0.0002071 0.98 41.35444 32.47711 27037653 0.353243 0.0021349 55105594 99.98650 100 30515895 84.67 48770148 NA NA NA NA NA NA
AnswerALS CASE_NEUDD018KAH 88045557 122378672 122378672 88045557 100 44020125 0.0003412 0.99 55.66305 44.06664 26965653 0.196328 0.0026667 34333115 99.99397 100 28593991 89.49 40078342 NA NA NA NA NA NA
AnswerALS CASE_NEUDE902GCT 99937040 135441084 135441084 99937040 100 49965149 0.0002740 0.99 57.04999 46.88175 31750639 0.195966 0.0027189 35504044 99.99325 100 33903856 89.67 45708501 NA NA NA NA NA NA
AnswerALS CASE_NEUDG000ZG5 100589599 165876997 165876997 100589599 100 50291866 0.0006254 0.99 46.05712 27.37350 22704273 0.205570 0.0027085 65287398 99.99417 100 24022760 86.49 44142529 NA NA NA NA NA NA
AnswerALS CASE_NEUDG272XWC 119792730 177927759 177927759 119792730 100 59890533 0.0006492 1.00 44.32943 35.83447 31883115 0.312701 0.0019648 58135029 99.99026 100 36165777 85.26 52442197 NA NA NA NA NA NA
AnswerALS CASE_NEUDH063DEA 105591880 147314413 147314413 105591880 100 52792270 0.0001292 0.97 43.49162 44.14237 32517163 0.368034 0.0018514 41722533 99.99305 100 34872581 88.71 47660863 NA NA NA NA NA NA
AnswerALS CASE_NEUDM949BAR 128202048 287681995 287681995 128202048 100 64098089 0.0001448 1.03 25.96516 19.68364 28314124 0.380233 0.0022874 159479947 99.99542 100 32796971 77.47 51012285 NA NA NA NA NA NA
AnswerALS CASE_NEUDP155HFH 139462948 169095371 169095371 139462948 100 69727255 0.0001219 0.98 60.02936 46.56030 39368193 0.248814 0.0018828 29632423 99.99395 100 42287242 91.81 64911812 NA NA NA NA NA NA
AnswerALS CASE_NEUDT709YHN 98823893 124576566 124576566 98823893 100 49409281 0.0001435 1.01 62.71525 43.64291 27185855 0.182869 0.0025115 25752673 99.99461 100 29035636 91.79 45965043 NA NA NA NA NA NA
AnswerALS CASE_NEUDY534KGP 141589390 224129099 224129099 141589390 100 70790345 0.0005739 0.98 38.78086 31.40492 35195960 0.357183 0.0021470 82539709 99.99386 100 38758487 85.07 61667082 NA NA NA NA NA NA
AnswerALS CASE_NEUDZ473EGM 154600775 199257878 199257878 154600775 100 77292269 0.0001501 0.98 54.35758 42.13185 41979848 0.273593 0.0020343 44657103 99.98950 100 45298101 89.96 70716346 NA NA NA NA NA NA
AnswerALS CASE_NEUEB422WW0 130660148 179922487 179922487 130660148 100 65326217 0.0002187 0.97 55.14692 45.24011 40700856 0.211997 0.0026283 49262339 99.99410 100 42774565 89.96 59731414 NA NA NA NA NA NA
AnswerALS CASE_NEUEC400NYR 125412392 189213757 189213757 125412392 100 62698769 0.0000618 0.98 46.63567 32.48969 30741078 0.263394 0.0020064 63801365 99.98816 100 33532156 85.61 55448738 NA NA NA NA NA NA
AnswerALS CASE_NEUEK191WYC 106345287 143788123 143788123 106345287 100 53169399 0.0003434 0.99 56.49555 44.95985 32325352 0.206117 0.0025269 37442836 99.99390 100 34889663 89.84 48514495 NA NA NA NA NA NA
AnswerALS CASE_NEUEM029XXZ 93028028 116184964 116184964 93028028 100 46511187 0.0000987 0.98 64.36809 45.35590 26350014 0.168057 0.0025941 23156936 99.99392 100 27645965 91.84 43343592 NA NA NA NA NA NA
AnswerALS CASE_NEUEM720BUU 86141784 131324319 131324319 86141784 100 43068135 0.0002889 0.97 46.29251 40.06190 26307070 0.259890 0.0029109 45182535 99.99360 100 29496177 86.04 37987180 NA NA NA NA NA NA
AnswerALS CASE_NEUEN017PCJ 130567564 222562143 222562143 130567564 100 65279499 0.0005546 0.98 38.82526 29.48605 32814502 0.304728 0.0020111 91994579 99.99344 100 35304279 84.03 56203623 NA NA NA NA NA NA
AnswerALS CASE_NEUEN476CLW 93313194 124980814 124980814 93313194 100 46653389 0.0002496 0.98 58.79835 45.51679 28445515 0.179232 0.0028058 31667620 99.99312 100 30075286 90.15 42774630 NA NA NA NA NA NA
AnswerALS CASE_NEUET072VDG 141595402 188283258 188283258 141595402 100 70794354 0.0001037 1.00 48.77956 45.04774 42410775 0.326791 0.0020269 46687856 99.99527 100 46245461 89.47 64389846 NA NA NA NA NA NA
AnswerALS CASE_NEUEU318NY2 134884750 201782160 201782160 134884750 100 67439023 0.0003835 1.01 43.29325 34.36975 34677910 0.323295 0.0020267 66897410 99.99503 100 38364153 86.00 59255159 NA NA NA NA NA NA
AnswerALS CASE_NEUEU558MNK 100521886 138251806 138251806 100521886 100 50257610 0.0002044 1.00 58.04566 40.34897 27893309 0.172240 0.0027409 37729920 99.99337 100 28934684 90.09 46268251 NA NA NA NA NA NA
AnswerALS CASE_NEUEY478NZP 123856364 161856132 161856132 123856364 100 61925206 0.0001457 1.01 49.49657 48.32963 39114279 0.326938 0.0018693 37999768 99.99519 100 43542860 89.22 56068266 NA NA NA NA NA NA
AnswerALS CASE_NEUFB989DT1 97111909 119493426 119493426 97111909 100 48553082 0.0003310 0.98 65.46732 42.98284 25682366 0.167866 0.0025665 22381517 99.99408 100 27242345 92.20 45373156 NA NA NA NA NA NA
AnswerALS CASE_NEUFH122WN7 139072399 163898369 163898369 139072399 100 69531586 0.0000398 0.98 64.35023 36.80086 30160047 0.219188 0.0019883 24825970 99.99337 100 30026682 93.49 65888103 NA NA NA NA NA NA
AnswerALS CASE_NEUFH461AAN 136572099 178778483 178778483 136572099 100 68282467 0.0002066 0.99 51.64257 38.98675 34851914 0.298697 0.0023940 42206384 99.99475 100 37275738 89.44 62183816 NA NA NA NA NA NA
AnswerALS CASE_NEUFU395MJD 106078669 150927010 150927010 106078669 100 53033252 0.0003335 0.97 46.37928 36.14942 27282828 0.311878 0.0020394 44848341 99.98853 100 30319443 87.29 47215106 NA NA NA NA NA NA
AnswerALS CASE_NEUFV237VCZ 116591551 142251705 142251705 116591551 100 58289922 0.0000931 0.98 60.75871 40.78029 29008424 0.233622 0.0020568 25660154 99.98996 100 29905603 91.78 54588104 NA NA NA NA NA NA
AnswerALS CASE_NEUFX386KMB 136454440 179241166 179241166 136454440 100 68222312 0.0000788 0.98 52.12221 43.88143 39329613 0.289722 0.0020814 42786726 99.99281 100 42433048 89.66 62381253 NA NA NA NA NA NA
AnswerALS CASE_NEUFY342UNG 118184565 150571375 150571375 118184565 100 59087606 0.0001005 0.99 58.35599 38.33532 28863430 0.230310 0.0018508 32386810 99.99209 100 31272225 89.91 54126474 NA NA NA NA NA NA
AnswerALS CASE_NEUGD965XVD 136583771 169896591 169896591 136583771 100 68287240 0.0002035 1.02 59.11176 45.68885 38814619 0.241102 0.0019518 33312820 99.99320 100 40989816 91.63 63555884 NA NA NA NA NA NA
AnswerALS CASE_NEUGE540TC4 75422741 95453478 95453478 75422741 100 37708985 0.0004707 1.00 64.92686 41.39750 19758910 0.150972 0.0026750 20030737 99.99367 100 20586436 91.90 35209660 NA NA NA NA NA NA
AnswerALS CASE_NEUGH995TFK 133045485 181931315 181931315 133045485 100 66515692 0.0000703 0.97 45.06227 42.23993 38428248 0.358487 0.0017872 48885830 99.98940 100 42594183 87.29 59472955 NA NA NA NA NA NA
AnswerALS CASE_NEUGJ081HKR 92827431 129592427 129592427 92827431 100 46411223 0.0002330 0.99 55.89339 40.40376 26181432 0.187137 0.0026103 36764996 99.99463 100 28115190 89.63 42254938 NA NA NA NA NA NA
AnswerALS CASE_NEUGL543NJ1 122243099 155846140 155846140 122243099 100 61116951 0.0001317 1.01 57.60356 38.98401 30380271 0.239767 0.0019417 33603041 99.99248 100 32357464 90.50 56279458 NA NA NA NA NA NA
AnswerALS CASE_NEUGP781PDU 99089507 123260123 123260123 99089507 100 49542192 0.0000507 0.97 63.37958 48.03670 29606571 0.184248 0.0024666 24170616 99.99483 100 31353374 91.95 46168118 NA NA NA NA NA NA
AnswerALS CASE_NEUGR121TFD 141091397 199599129 199599129 141091397 100 70536352 0.0001659 0.98 49.49694 36.83002 36761388 0.270829 0.0021551 58507732 99.98675 100 38723194 86.77 63614335 NA NA NA NA NA NA
AnswerALS CASE_NEUGR539MVT 134594246 172095822 172095822 134594246 100 67286121 0.0001557 1.00 52.87871 45.50994 39167316 0.300302 0.0021235 37501576 99.98365 100 42249514 89.43 61521240 NA NA NA NA NA NA
AnswerALS CASE_NEUGW326BRV 86942871 119710782 119710782 86942871 100 43469101 0.0002033 0.98 56.16165 39.44430 23610810 0.195022 0.0026380 32767911 99.99463 100 25361092 89.90 39656424 NA NA NA NA NA NA
AnswerALS CASE_NEUGW340YEB 136692973 183476162 183476162 136692973 100 68340429 0.0000880 1.00 51.60555 38.39680 35227745 0.279955 0.0019997 46783189 99.99114 100 38284910 89.09 62053078 NA NA NA NA NA NA
AnswerALS CASE_NEUHB491NGF 145522197 202221470 202221470 145522197 100 72753784 0.0002094 0.96 50.41580 31.63419 31988783 0.272387 0.0020442 56699273 99.98995 100 32812161 89.01 66227888 NA NA NA NA NA NA
AnswerALS CASE_NEUHG644RYB 138979998 201813224 201813224 138979998 100 69482706 0.0001692 1.01 45.87918 38.66221 39017272 0.304173 0.0018454 62833226 99.98950 100 43918370 85.05 60646533 NA NA NA NA NA NA
AnswerALS CASE_NEUHG791RV5 119400996 160767092 160767092 119400996 100 59697027 0.0000261 0.99 56.18658 42.85333 34448962 0.214817 0.0025435 41366096 99.99419 100 36903652 90.01 54523059 NA NA NA NA NA NA
AnswerALS CASE_NEUHK991AVP 150076387 203632648 203632648 150076387 100 75035119 0.0003553 0.99 45.16991 45.32742 46152868 0.363986 0.0018715 53556261 99.99590 100 51372601 88.06 67327991 NA NA NA NA NA NA
AnswerALS CASE_NEUHL999WWT 120914707 152068342 152068342 120914707 100 60453335 0.0002409 0.99 58.29780 42.58072 32378390 0.242050 0.0020147 31153635 99.99335 100 34087609 91.26 56126841 NA NA NA NA NA NA
AnswerALS CASE_NEUHM532NDD 132018194 177570876 177570876 132018194 100 66004538 0.0005658 0.99 53.15327 33.04001 29336787 0.257687 0.0020835 45552682 99.99309 100 31431334 89.17 60004909 NA NA NA NA NA NA
AnswerALS CASE_NEUHT569HT1 135726690 175838065 175838065 135726690 100 67856787 0.0001545 0.98 53.70584 36.81147 32367583 0.278507 0.0021176 40111375 99.99034 100 34696832 89.43 62178209 NA NA NA NA NA NA
AnswerALS CASE_NEUHV216EHA 137327199 187736616 187736616 137327199 100 68658564 0.0011124 0.96 51.74819 31.40976 29486017 0.266897 0.0020767 50409417 99.99267 100 31516294 88.75 62223182 NA NA NA NA NA NA
AnswerALS CASE_NEUHW530WD8 142706149 186097772 186097772 142706149 100 71346968 0.0001573 0.98 54.96032 43.72086 40685469 0.257348 0.0020625 43391623 99.99144 100 42259547 90.23 65688979 NA NA NA NA NA NA
AnswerALS CASE_NEUHW590KBH 87895366 120494665 120494665 87895366 100 43945090 0.0001100 0.98 57.59010 39.21984 23630275 0.178782 0.0025832 32599299 99.99410 100 25159813 89.88 40130196 NA NA NA NA NA NA
AnswerALS CASE_NEUHY206ZEQ 112630093 177166290 177166290 112630093 100 56312448 0.0012134 0.99 39.86670 38.70032 34283660 0.342164 0.0019487 64536197 99.99539 100 38206988 85.64 49149528 NA NA NA NA NA NA
AnswerALS CASE_NEUHZ302VU4 84819581 110724093 110724093 84819581 100 42407446 0.0003190 1.00 58.77952 51.52982 28529537 0.203833 0.0025028 25904512 99.99447 100 30685204 90.34 38920358 NA NA NA NA NA NA
AnswerALS CASE_NEUJA217MTJ 138544788 180023548 180023548 138544788 100 69268627 0.0001135 1.01 61.97741 29.35444 26423870 0.168603 0.0026456 41478760 99.99456 100 27865782 91.26 64185561 NA NA NA NA NA NA
AnswerALS CASE_NEUJA666PYD 104992916 179578594 179578594 104992916 100 52492856 0.0001505 0.97 42.87717 30.33617 27240233 0.229110 0.0027915 74585678 99.99314 100 29473424 84.84 45410352 NA NA NA NA NA NA
AnswerALS CASE_NEUJC191RLE 134351533 169112893 169112893 134351533 100 67171099 0.0004095 0.99 58.06424 36.96069 31254937 0.244700 0.0020588 34761360 99.99305 100 33284137 90.83 62105731 NA NA NA NA NA NA
AnswerALS CASE_NEUJG311WGV 129764735 173924387 173924387 129764735 100 64879037 0.0002634 0.98 50.35555 38.41671 33409743 0.299301 0.0020763 44159652 99.99487 100 37635711 88.24 58253244 NA NA NA NA NA NA
AnswerALS CASE_NEUJG885PY7 141363192 207769282 207769282 141363192 100 70672574 0.0004961 0.99 45.29718 35.89114 37290108 0.305882 0.0021327 66406090 99.98724 100 39751751 86.43 62682976 NA NA NA NA NA NA
AnswerALS CASE_NEUJH197AK2 109692064 148477602 148477602 109692064 100 54840601 0.0000835 1.01 50.42878 48.36931 35912880 0.290581 0.0018832 38785538 99.99010 100 39219267 88.36 49489164 NA NA NA NA NA NA
AnswerALS CASE_NEUJK720JCL 145196285 176658442 176658442 145196285 100 72593038 0.0001203 0.98 58.35053 41.40399 36574311 0.266350 0.0022999 31462157 99.99297 100 38573347 92.26 67904327 NA NA NA NA NA NA
AnswerALS CASE_NEUJL547WVQ 122518635 147759823 147759823 122518635 100 61252132 0.0000491 1.07 56.70514 46.87074 34632151 0.292459 0.0018165 25241188 99.98827 100 35492615 92.56 57611614 NA NA NA NA NA NA
AnswerALS CASE_NEUJL595JAZ 125569663 167641984 167641984 125569663 100 62781255 0.0001647 1.00 49.09008 39.12172 32794270 0.317243 0.0024428 42072321 99.99430 100 35920670 88.09 56604191 NA NA NA NA NA NA
AnswerALS CASE_NEUJP935AVF 133932079 201524424 201524424 133932079 100 66962632 0.0004649 0.99 42.24562 30.52310 30757338 0.337322 0.0021899 67592345 99.99491 100 34475263 85.68 58630869 NA NA NA NA NA NA
AnswerALS CASE_NEUJX780XXK 132644761 163932667 163932667 132644761 100 66316933 0.0001693 1.00 59.09920 38.90757 31893879 0.245205 0.0019813 31287906 99.99179 100 32976255 91.64 61928100 NA NA NA NA NA NA
AnswerALS CASE_NEUJX990GR5 152756972 180280188 180280188 152756972 100 76370797 0.0003500 0.98 60.56161 38.67019 34861001 0.262740 0.0019740 27523216 99.98993 100 37160120 92.49 71699955 NA NA NA NA NA NA
AnswerALS CASE_NEUJY426MBU 163506082 212057895 212057895 163506082 100 81747885 0.0000659 0.96 55.88217 38.63594 40967948 0.250772 0.0019916 48551813 99.99369 100 42713301 90.91 75805318 NA NA NA NA NA NA
AnswerALS CASE_NEUJY536DKF 130996985 161559410 161559410 130996985 100 65493732 0.0001393 0.96 59.05377 42.66486 34467201 0.247774 0.0020449 30562425 99.99273 100 36355288 91.51 60915279 NA NA NA NA NA NA
AnswerALS CASE_NEUKA860NUG 95743148 149986716 149986716 95743148 100 47868100 0.0004797 0.99 39.72778 32.51799 24388292 0.343615 0.0022024 54243568 99.99274 100 28045765 83.39 41004845 NA NA NA NA NA NA
AnswerALS CASE_NEUKD025JPF 73470692 95420234 95420234 73470692 100 36733163 0.0003883 1.00 61.46689 46.42426 22150320 0.170845 0.0026557 21949542 99.99406 100 23648413 91.00 33925482 NA NA NA NA NA NA
AnswerALS CASE_NEUKP160HX8 158114922 219097462 219097462 158114922 100 79053571 0.0000658 1.00 44.77145 40.20348 44044684 0.354843 0.0020222 60982540 99.99508 100 48852294 87.81 70714096 NA NA NA NA NA NA
AnswerALS CASE_NEUKR376CW3 137592744 180066208 180066208 137592744 100 68793025 0.0002550 1.01 52.27950 38.76256 34901012 0.291103 0.0020278 42473464 99.99513 100 37955194 89.17 62403770 NA NA NA NA NA NA
AnswerALS CASE_NEUKV547CFA 106270699 173079851 173079851 106270699 100 53131757 0.0001257 1.01 37.97373 32.16386 27836633 0.347247 0.0020279 66809152 99.99324 100 32569899 82.44 45019350 NA NA NA NA NA NA
AnswerALS CASE_NEUKY704JVA 111957315 145492330 145492330 111957315 100 55973716 0.0006706 0.99 53.27409 44.06555 32059068 0.281775 0.0018965 33535015 99.99117 100 34918698 88.69 51063996 NA NA NA NA NA NA
AnswerALS CASE_NEULA694DDC 144121470 210976422 210976422 144121470 100 72052030 0.0001136 0.99 32.83201 39.23243 41391076 0.496468 0.0019312 66854952 99.98792 100 46414165 85.78 63306620 NA NA NA NA NA NA
AnswerALS CASE_NEULA777DBT 145235062 185554062 185554062 145235062 100 72609573 0.0001060 0.99 57.47245 38.64274 35855491 0.238996 0.0021044 40319000 99.98904 100 37728047 90.04 66935925 NA NA NA NA NA NA
AnswerALS CASE_NEULD354RZB 130303603 171222929 171222929 130303603 100 65147360 0.0000794 0.99 52.14630 39.73101 34017084 0.290105 0.0019778 40919326 99.99318 100 37816668 88.81 58989271 NA NA NA NA NA NA
AnswerALS CASE_NEULH729AU2 132185143 188457240 188457240 132185143 100 66082206 0.0000322 1.02 33.72764 32.90749 31013438 0.497084 0.0022970 56272097 99.98432 100 33250669 86.85 59187708 NA NA NA NA NA NA
AnswerALS CASE_NEULL588ALG 101192464 129328744 129328744 101192464 100 50592428 0.0004602 1.03 62.52614 40.65428 26290767 0.171396 0.0025575 28136280 99.99248 100 27554179 91.05 46819320 NA NA NA NA NA NA
AnswerALS CASE_NEULL648LJ1 152013999 189349623 189349623 152013999 100 75998771 0.0003482 0.99 56.32040 46.09657 43647051 0.275342 0.0021868 37335624 99.98917 100 47298299 90.61 70333861 NA NA NA NA NA NA
AnswerALS CASE_NEULP998KDJ 101414493 129829996 129829996 101414493 100 50702318 0.0001817 1.00 57.38737 39.83596 25862178 0.238810 0.0019215 28415503 99.99028 100 27433069 90.22 46667209 NA NA NA NA NA NA
AnswerALS CASE_NEULT851ENP 141787116 182679467 182679467 141787116 100 70890034 0.0000863 0.98 52.31735 45.64324 41692465 0.301362 0.0019864 40892351 99.99503 100 44820562 90.51 65314488 NA NA NA NA NA NA
AnswerALS CASE_NEULY177TTN 88184032 140832260 140832260 88184032 100 44089217 0.0001702 0.98 45.99328 35.86896 25258960 0.229827 0.0026625 52648228 99.99365 100 27538571 85.82 38673250 NA NA NA NA NA NA
AnswerALS CASE_NEULY328CRJ 124827649 178583027 178583027 124827649 100 62409884 0.0001362 0.99 45.38943 39.45594 35233132 0.322612 0.0020742 53755378 99.99369 100 38907414 87.51 55659392 NA NA NA NA NA NA
AnswerALS CASE_NEULZ548ZXV 116550540 157670085 157670085 116550540 100 58269845 0.0006271 1.02 50.82802 39.63846 31252626 0.285243 0.0021817 41119545 99.99069 100 34000171 88.43 52791572 NA NA NA NA NA NA
AnswerALS CASE_NEUMB242CLN 146219969 188982330 188982330 146219969 100 73094377 0.0001099 0.97 53.25336 41.38281 39111622 0.285622 0.0020325 42762361 99.97865 100 42594423 89.14 66786201 NA NA NA NA NA NA
AnswerALS CASE_NEUME498PCJ 121179342 166957105 166957105 121179342 100 60586895 0.0003321 0.98 53.63860 38.22758 31913320 0.232192 0.0024516 45777763 99.99542 100 35558756 88.60 54433039 NA NA NA NA NA NA
AnswerALS CASE_NEUMH634MKT 149214391 209805138 209805138 149214391 100 74603299 0.0020155 1.02 46.51324 39.06467 40982048 0.318690 0.0020759 60590747 99.99478 100 44454595 87.85 66723213 NA NA NA NA NA NA
AnswerALS CASE_NEUMN012EVP 122953745 152285269 152285269 122953745 100 61473583 0.0004007 0.97 60.87585 40.63853 30944925 0.222147 0.0019786 29331524 99.99465 100 32093482 92.10 57458694 NA NA NA NA NA NA
AnswerALS CASE_NEUMW598YMT 148697107 211131558 211131558 148697107 100 74341725 0.0004545 0.97 45.45767 35.42568 37401266 0.327205 0.0021479 62434451 99.99082 100 40987087 86.39 66263817 NA NA NA NA NA NA
AnswerALS CASE_NEUMY871DGF 139888957 164950585 164950585 139888957 100 69938355 0.0000798 0.99 64.38220 41.02218 33836284 0.218205 0.0019914 25061628 99.99125 100 35805638 92.48 65655990 NA NA NA NA NA NA
AnswerALS CASE_NEUNA248WXL 87881681 112756521 112756521 87881681 100 43938255 0.0003365 0.98 63.36786 37.94840 21395900 0.158051 0.0026177 24874840 99.99412 100 22601559 91.86 40898290 NA NA NA NA NA NA
AnswerALS CASE_NEUNG326MFP 141420621 188366517 188366517 141420621 100 70704595 0.0001198 0.97 51.47303 40.77300 38404802 0.288874 0.0019689 46945896 99.99192 100 41918606 89.03 64097084 NA NA NA NA NA NA
AnswerALS CASE_NEUNJ155KYL 139821585 183237512 183237512 139821585 100 69907930 0.0001016 1.03 50.34089 44.02644 40338225 0.315424 0.0018692 43415927 99.99591 100 44436014 89.26 63359785 NA NA NA NA NA NA
AnswerALS CASE_NEUNJ938DUL 110373409 146981217 146981217 110373409 100 55180998 0.0002221 1.01 49.53905 42.27752 31073805 0.313882 0.0020983 36607808 99.98966 100 34163950 87.65 49706589 NA NA NA NA NA NA
AnswerALS CASE_NEUNL303HLF 125099316 228966770 228966770 125099316 100 62546398 0.0001992 1.00 32.27064 29.37712 33633585 0.378200 0.0020683 103867454 99.99479 100 36878172 82.03 52488696 NA NA NA NA NA NA
AnswerALS CASE_NEUNL415AFW 92867967 133667390 133667390 92867967 100 46431277 0.0008440 0.97 52.02197 42.72272 28554762 0.219845 0.0027121 40799423 99.99417 100 30330975 88.33 41786405 NA NA NA NA NA NA
AnswerALS CASE_NEUNR020KV6 115301323 164150667 164150667 115301323 100 57647868 0.0002172 0.97 46.35115 37.01777 30383974 0.312230 0.0020360 48849344 99.99515 100 33596521 87.46 51460383 NA NA NA NA NA NA
AnswerALS CASE_NEUNZ171UYF 155580787 201349190 201349190 155580787 100 77786615 0.0000477 1.00 54.53630 41.63565 41918494 0.268249 0.0020768 45768403 99.99514 100 43804088 90.97 71885848 NA NA NA NA NA NA
AnswerALS CASE_NEUPG593UTV 126721699 179908913 179908913 126721699 100 63355853 0.0002942 0.98 43.44807 36.26768 32627194 0.356489 0.0021263 53187214 99.99211 100 36485890 86.39 56098842 NA NA NA NA NA NA
AnswerALS CASE_NEUPK546ZLD 127719209 173514278 173514278 127719209 100 63853530 0.0006982 0.98 52.70728 41.76322 36236208 0.255609 0.0019434 45795069 99.99049 100 38892514 88.95 58161535 NA NA NA NA NA NA
AnswerALS CASE_NEUPM937TMY 114752546 154017532 154017532 114752546 100 57373291 0.0001371 1.00 48.91011 40.73999 31375051 0.317677 0.0020453 39264986 99.99480 100 33677004 89.09 52119903 NA NA NA NA NA NA
AnswerALS CASE_NEUPN525XEW 100061085 152901938 152901938 100061085 100 50027523 0.0011091 0.96 48.26096 37.85523 28942287 0.229381 0.0027257 52840853 99.99396 100 30587704 86.88 44430092 NA NA NA NA NA NA
AnswerALS CASE_NEUPR357AUF 140600115 188629695 188629695 140600115 100 70294764 0.0003826 1.01 50.96441 42.12141 39730312 0.290189 0.0020325 48029580 99.99247 100 42959648 88.51 63541475 NA NA NA NA NA NA
AnswerALS CASE_NEUPR600MBU 101661612 157059475 157059475 101661612 100 50828202 0.0006545 0.95 47.55700 38.91106 30558182 0.231348 0.0025577 55397863 99.99488 100 33189766 87.17 45072415 NA NA NA NA NA NA
AnswerALS CASE_NEUPY050ANK 125092895 173092975 173092975 125092895 100 62538321 0.0008399 0.97 47.48535 37.00170 32028248 0.316107 0.0021859 48000080 99.98701 100 34791092 87.00 56250544 NA NA NA NA NA NA
AnswerALS CASE_NEURA639MK8 88681385 174800313 174800313 88681385 100 44338192 0.0002404 0.99 35.38047 26.17944 22881914 0.261938 0.0026667 86118928 99.99436 100 25273046 81.23 36696280 NA NA NA NA NA NA
AnswerALS CASE_NEURF720KHA 127645475 214650164 214650164 127645475 100 63818250 0.0001552 1.02 37.19388 30.61430 32858913 0.341368 0.0020499 87004689 99.99297 100 36233250 84.23 54948319 NA NA NA NA NA NA
AnswerALS CASE_NEURJ362MXH 128821381 164937784 164937784 128821381 100 64406009 0.0002776 0.99 54.82691 32.31893 26655251 0.273043 0.0020595 36116403 99.99273 100 28257434 90.79 59538230 NA NA NA NA NA NA
AnswerALS CASE_NEURR881FKY 107640056 139900164 139900164 107640056 100 53817142 0.0001954 0.97 59.88210 38.77847 27126995 0.192805 0.0024546 32260108 99.99464 100 29184368 90.84 49514621 NA NA NA NA NA NA
AnswerALS CASE_NEURX315DYH 105760532 182500083 182500083 105760532 100 52875618 0.0002318 1.00 38.24761 32.14216 29332003 0.304415 0.0019613 76739551 99.99121 100 31862596 84.81 45743652 NA NA NA NA NA NA
AnswerALS CASE_NEURX909UL6 101253707 143049397 143049397 101253707 100 50623663 0.0003391 0.99 52.97698 43.28501 30961318 0.218807 0.0026655 41795690 99.99370 100 33363015 88.75 45735585 NA NA NA NA NA NA
AnswerALS CASE_NEUTA057AF6 145972936 182832898 182832898 145972936 100 72981892 0.0001730 0.98 57.41441 42.36811 38733887 0.255461 0.0019554 36859962 99.99373 100 39947509 92.03 68030270 NA NA NA NA NA NA
AnswerALS CASE_NEUTA689LN5 97978631 137960489 137960489 97978631 100 48986369 0.0000766 0.99 54.36726 45.44476 31349678 0.201869 0.0026863 39981858 99.99399 100 33057528 89.27 44471077 NA NA NA NA NA NA
AnswerALS CASE_NEUTB230DA3 127287620 167555194 167555194 127287620 100 63638375 0.0002299 0.99 51.77864 44.64902 37410054 0.293582 0.0021534 40267574 99.99146 100 41078024 88.53 57735990 NA NA NA NA NA NA
AnswerALS CASE_NEUTC791PVE 145218429 194002781 194002781 145218429 100 72602394 0.0001546 0.96 48.45311 42.66868 41393810 0.326557 0.0020144 48784352 99.99061 100 45961276 87.67 65228107 NA NA NA NA NA NA
AnswerALS CASE_NEUTD314VFT 118694774 199503383 199503383 118694774 100 59340190 0.0003396 1.01 40.55880 28.63025 28562306 0.283515 0.0019801 80808609 99.98787 100 31769329 84.10 51072663 NA NA NA NA NA NA
AnswerALS CASE_NEUTD713DE3 111654521 157067140 157067140 111654521 100 55824002 0.0001290 0.98 52.91439 42.42968 33323420 0.224722 0.0027149 45412619 99.99416 100 35928817 89.06 50602796 NA NA NA NA NA NA
AnswerALS CASE_NEUTD866EAH 124436305 180663402 180663402 124436305 100 62210277 0.0002514 0.98 44.24790 38.73755 34997730 0.329244 0.0021389 56227097 99.98734 100 39272084 85.83 54881137 NA NA NA NA NA NA
AnswerALS CASE_NEUTJ613AH9 72472964 98310077 98310077 72472964 100 36233970 0.0002277 0.99 59.58567 35.73748 17567925 0.161272 0.0026973 25837113 99.99307 100 18303686 90.13 33289122 NA NA NA NA NA NA
AnswerALS CASE_NEUTL257PNR 132701657 180494960 180494960 132701657 100 66347623 0.0002861 1.00 49.20961 39.11086 35298356 0.304793 0.0020186 47793303 99.99517 100 37791840 88.97 60066049 NA NA NA NA NA NA
AnswerALS CASE_NEUTL699WJ0 114658516 144969594 144969594 114658516 100 57324735 0.0010707 0.97 56.07008 44.57791 32315111 0.266599 0.0019060 30311078 99.99211 100 35710392 89.86 52348367 NA NA NA NA NA NA
AnswerALS CASE_NEUTM934BPY 129527421 171464767 171464767 129527421 100 64759198 0.0015967 1.00 53.80390 36.74346 31503263 0.261451 0.0020043 41937346 99.99303 100 34456215 89.53 59086995 NA NA NA NA NA NA
AnswerALS CASE_NEUTN952DDG 105873411 166179344 166179344 105873411 100 52933748 0.0003591 0.99 46.94140 33.50951 27844308 0.231224 0.0025588 60305933 99.99441 100 29696227 86.83 46944485 NA NA NA NA NA NA
AnswerALS CASE_NEUTU360YJY 116118985 143509356 143509356 116118985 100 58052735 0.0001467 1.01 57.95106 53.19941 38177862 0.259297 0.0017220 27390371 99.98836 100 41726408 90.06 53322943 NA NA NA NA NA NA
AnswerALS CASE_NEUUC458RFT 129847013 194034481 194034481 129847013 100 64917516 0.0001199 1.02 41.97888 34.38410 33362263 0.343356 0.0020920 64187468 99.99077 100 37273830 84.20 56817414 NA NA NA NA NA NA
AnswerALS CASE_NEUUD158CJF 104670750 132835531 132835531 104670750 100 52328344 0.0000158 0.97 53.12357 47.52401 31569214 0.300438 0.0018088 28164781 99.98657 100 35081615 88.71 47698947 NA NA NA NA NA NA
AnswerALS CASE_NEUUE852BB1 87313527 122251990 122251990 87313527 100 43654085 0.0000895 0.98 54.63034 43.88646 26827563 0.201953 0.0025186 34938463 99.99386 100 28952491 88.87 39423970 NA NA NA NA NA NA
AnswerALS CASE_NEUUF613PHL 126490792 162878061 162878061 126490792 100 63241442 0.0000430 0.97 52.54516 42.82306 34877131 0.298866 0.0021813 36387269 99.99375 100 38470412 89.41 57733762 NA NA NA NA NA NA
AnswerALS CASE_NEUUH658EYH 121126070 181119012 181119012 121126070 100 60560176 0.0006071 1.00 41.82229 39.10448 35414672 0.346869 0.0019553 59992942 99.99528 100 40091692 85.86 53030800 NA NA NA NA NA NA
AnswerALS CASE_NEUUJ507EAB 114321103 144750000 144750000 114321103 100 57157204 0.0000440 1.06 53.63220 47.14457 34123017 0.296042 0.0015816 30428897 99.99414 100 37643813 89.78 52034154 NA NA NA NA NA NA
AnswerALS CASE_NEUUL256UC9 119837015 165056579 165056579 119837015 100 59911454 0.0001191 0.98 53.36755 30.51364 25185391 0.235516 0.0021328 45219564 99.98823 100 27258314 87.95 54168228 NA NA NA NA NA NA
AnswerALS CASE_NEUUL292XRC 104836431 156852741 156852741 104836431 100 52409181 0.0003069 1.00 43.89086 33.23504 26069986 0.311924 0.0019622 52016310 99.98276 100 29882387 84.80 45819278 NA NA NA NA NA NA
AnswerALS CASE_NEUUL311NRQ 144461771 187508051 187508051 144461771 100 72226897 0.0001483 1.03 51.75003 41.70654 39103731 0.303675 0.0019373 43046280 99.99448 100 42363669 90.08 66008915 NA NA NA NA NA NA
AnswerALS CASE_NEUUP280KXL 118516272 156079810 156079810 118516272 100 59254381 0.0001999 0.99 54.93796 41.02595 32018652 0.250312 0.0019529 37563538 99.99366 100 33948150 89.62 54110646 NA NA NA NA NA NA
AnswerALS CASE_NEUUU506WZF 138573134 292249673 292249673 138573134 100 69279224 0.0006337 0.99 29.33627 18.68155 27300803 0.342525 0.0023071 153676539 99.98940 100 30195009 78.78 56290277 NA NA NA NA NA NA
AnswerALS CASE_NEUUZ216XY8 117115830 153394704 153394704 117115830 100 58553043 0.0003654 1.01 53.12807 42.10338 32295500 0.276408 0.0019538 36278874 99.99168 100 35552913 89.03 53409559 NA NA NA NA NA NA
AnswerALS CASE_NEUVD687XD8 127850466 196983862 196983862 127850466 100 63918317 0.0002929 1.01 41.30500 33.27007 32772166 0.333570 0.0022399 69133396 99.98918 100 36669301 84.14 55483568 NA NA NA NA NA NA
AnswerALS CASE_NEUVF888UHM 87839503 123440383 123440383 87839503 100 43916958 0.0008791 1.01 55.05094 38.51858 23775161 0.194150 0.0027037 35600880 99.99364 100 25076486 88.39 39713751 NA NA NA NA NA NA
AnswerALS CASE_NEUVJ560JGZ 145026604 169004770 169004770 145026604 100 72508859 0.0001747 0.99 66.23438 37.93196 32055485 0.205332 0.0020462 23978166 99.99387 100 32639281 93.31 68598571 NA NA NA NA NA NA
AnswerALS CASE_NEUVM674HUA 112397326 158281937 158281937 112397326 100 56194993 0.0001695 1.00 50.24582 44.73241 35403908 0.263150 0.0026860 45884611 99.99347 100 38967578 87.97 50368377 NA NA NA NA NA NA
AnswerALS CASE_NEUVN746WKV 113418563 166319216 166319216 113418563 100 56705806 0.0000901 1.00 48.88816 38.69327 32179025 0.250970 0.0026661 52900653 99.99387 100 34899811 87.12 50451695 NA NA NA NA NA NA
AnswerALS CASE_NEUVP060WFG 144863978 187399644 187399644 144863978 100 72426514 0.0000170 0.99 49.74931 43.87856 41117626 0.333074 0.0020505 42535666 99.99244 100 45474655 88.88 65686991 NA NA NA NA NA NA
AnswerALS CASE_NEUVR636VTP 128629292 171359932 171359932 128629292 100 64309737 0.0001487 1.00 53.73263 38.45949 32954754 0.258677 0.0020067 42730640 99.99237 100 35787049 89.32 58705014 NA NA NA NA NA NA
AnswerALS CASE_NEUVR814YCY 144773359 197542865 197542865 144773359 100 72382408 0.0004202 1.00 50.77449 33.73113 33318593 0.281012 0.0023057 52769506 99.99410 100 34471604 89.47 65992995 NA NA NA NA NA NA
AnswerALS CASE_NEUVU735HU6 123502082 187698709 187698709 123502082 100 61747675 0.0003588 0.99 42.95702 34.74852 32612974 0.315037 0.0023181 64196627 99.99455 100 34653270 86.96 54922335 NA NA NA NA NA NA
AnswerALS CASE_NEUVV225XKB 123111385 155952079 155952079 123111385 100 61551693 0.0003383 1.00 54.53868 45.87263 35772048 0.283807 0.0020836 32840694 99.99350 100 37689921 91.00 56974263 NA NA NA NA NA NA
AnswerALS CASE_NEUVW680LPK 118581069 153225477 153225477 118581069 100 59284066 0.0003044 0.99 55.01467 45.87971 35153671 0.262525 0.0018957 34644408 99.98909 100 38389290 89.49 54123971 NA NA NA NA NA NA
AnswerALS CASE_NEUVW999FP9 122111979 175530863 175530863 122111979 100 61050651 0.0000599 1.00 48.28043 41.87448 36754568 0.275443 0.0018434 53418884 99.99126 100 39758243 87.43 54642824 NA NA NA NA NA NA
AnswerALS CASE_NEUVX902YNL 105687552 141270293 141270293 105687552 100 52838977 0.0003394 0.95 55.41355 31.70045 22393705 0.231272 0.0019910 35582741 99.99092 100 24062627 89.75 48398706 NA NA NA NA NA NA
AnswerALS CASE_NEUWD538KT3 93128892 129580487 129580487 93128892 100 46561423 0.0001520 0.97 55.12257 46.72140 30272812 0.202011 0.0025389 36451595 99.99351 100 32314676 89.32 42289028 NA NA NA NA NA NA
AnswerALS CASE_NEUWD946RDA 149520819 197641724 197641724 149520819 100 74753779 0.0002987 0.96 49.86001 43.02003 42517032 0.316072 0.0020719 48120905 99.99113 100 45622870 88.81 68185631 NA NA NA NA NA NA
AnswerALS CASE_NEUWH380YHV 118758017 154302029 154302029 118758017 100 59375307 0.0002332 0.99 56.59547 42.23046 32583607 0.238610 0.0018427 35544012 99.99377 100 34472568 90.88 54730470 NA NA NA NA NA NA
AnswerALS CASE_NEUWH955FJF 130639547 170232499 170232499 130639547 100 65312616 0.0001261 1.01 51.82487 39.11938 33300864 0.300246 0.0022484 39592952 99.98904 100 36381430 89.03 59642239 NA NA NA NA NA NA
AnswerALS CASE_NEUWJ389FC7 120192862 150666058 150666058 120192862 100 60092014 0.0000771 0.99 57.07302 43.05931 32440780 0.260635 0.0019176 30473196 99.99265 100 34827714 90.90 55551131 NA NA NA NA NA NA
AnswerALS CASE_NEUWM344ZLM 117831195 162934462 162934462 117831195 100 58912499 0.0002679 0.99 47.54644 36.20085 29493516 0.317124 0.0020166 45103267 99.99474 100 33397586 87.79 52677231 NA NA NA NA NA NA
AnswerALS CASE_NEUWP426NBR 104117727 136600495 136600495 104117727 100 52055846 0.0001242 0.95 60.07319 40.07443 27372491 0.182672 0.0026510 32482768 99.99420 100 28549535 90.96 48071230 NA NA NA NA NA NA
AnswerALS CASE_NEUWX167DAH 123682005 192704366 192704366 123682005 100 61834940 0.0001177 1.00 43.57415 37.02141 35674317 0.289182 0.0018338 69022361 99.99020 100 39765447 85.55 54107517 NA NA NA NA NA NA
AnswerALS CASE_NEUWY079WUH 129106543 181255681 181255681 129106543 100 64541424 0.0003487 0.98 40.01595 37.65129 34129175 0.412852 0.0023745 52149138 99.98165 100 36559926 87.00 58040835 NA NA NA NA NA NA
AnswerALS CASE_NEUWZ614ARQ 106843000 145508107 145508107 106843000 100 53419244 0.0002842 0.99 47.92555 42.08033 30616507 0.320886 0.0020071 38665107 99.99578 100 33688160 88.80 48202453 NA NA NA NA NA NA
AnswerALS CASE_NEUXD985ZU1 140301006 196956825 196956825 140301006 100 70146701 0.0000676 0.99 45.17465 36.03483 35488642 0.339938 0.0021713 56655819 99.99458 100 38729715 87.42 62695888 NA NA NA NA NA NA
AnswerALS CASE_NEUXE491RMM 97865811 118906208 118906208 97865811 100 48930212 0.0002695 0.98 66.82962 45.56580 27091815 0.161633 0.0026411 21040397 99.99450 100 28413979 92.38 45870390 NA NA NA NA NA NA
AnswerALS CASE_NEUXG265ME9 129621756 168423467 168423467 129621756 100 64806369 0.0005600 1.00 53.74925 41.77200 35179399 0.275283 0.0019760 38801711 99.99304 100 37190260 90.24 59421241 NA NA NA NA NA NA
AnswerALS CASE_NEUXH833LL4 142418106 190308209 190308209 142418106 100 71203163 0.0004520 1.01 50.06242 45.10139 42919477 0.306045 0.0020634 47890103 99.99173 100 46255615 89.75 65035209 NA NA NA NA NA NA
AnswerALS CASE_NEUXP289KRC 137919894 180193491 180193491 137919894 100 68955155 0.0000422 0.98 56.83071 36.80424 33161771 0.230765 0.0020719 42273597 99.99305 100 33565706 91.30 64019350 NA NA NA NA NA NA
AnswerALS CASE_NEUXP495XE2 144883140 207898467 207898467 144883140 100 72437782 0.0005885 0.99 46.52462 35.14467 36534422 0.305425 0.0021574 63015327 99.99477 100 38386537 87.90 64915635 NA NA NA NA NA NA
AnswerALS CASE_NEUXP595FFP 82882330 112629927 112629927 82882330 100 41439054 0.0004402 0.97 57.41643 43.96293 24758914 0.187966 0.0024695 29747597 99.99491 100 26423196 90.13 37877172 NA NA NA NA NA NA
AnswerALS CASE_NEUXV122FN3 128046620 164194973 164194973 128046620 100 64017537 0.0001862 1.00 55.16521 46.44593 38134683 0.267302 0.0018444 36148353 99.99098 100 41583014 89.72 58733300 NA NA NA NA NA NA
AnswerALS CASE_NEUXX361RUG 107229021 133348579 133348579 107229021 100 53611368 0.0003016 0.99 63.68358 48.23219 32160375 0.181221 0.0026846 26119558 99.99414 100 33003046 92.07 50204894 NA NA NA NA NA NA
AnswerALS CASE_NEUYC055XPZ 138951866 173601788 173601788 138951866 100 69470318 0.0001920 0.99 55.76776 40.19634 34893729 0.279873 0.0020410 34649922 99.99192 100 37040582 91.22 64543705 NA NA NA NA NA NA
AnswerALS CASE_NEUYC303AJY 120708861 161874054 161874054 120708861 100 60350667 0.0004616 0.98 51.12615 39.61285 32063539 0.286988 0.0021230 41165193 99.99376 100 34113253 90.06 55283224 NA NA NA NA NA NA
AnswerALS CASE_NEUYD306HAB 127940942 182627299 182627299 127940942 100 63946168 0.0002491 1.01 36.74887 40.42930 36932268 0.451589 0.0019820 54686357 99.96201 100 42007862 83.18 56076091 NA NA NA NA NA NA
AnswerALS CASE_NEUYG208KVV 124891243 199498682 199498682 124891243 100 62442357 0.0001144 0.99 38.73081 31.53442 31456954 0.351701 0.0021026 74607439 99.99477 100 35299541 84.26 54046799 NA NA NA NA NA NA
AnswerALS CASE_NEUYG298CA9 123272477 157809619 157809619 123272477 100 61632259 0.0002451 0.97 53.71753 48.08596 37944789 0.287246 0.0019546 34537142 99.99354 100 41968903 89.21 55941940 NA NA NA NA NA NA
AnswerALS CASE_NEUYH924UCE 119170920 163713959 163713959 119170920 100 59578923 0.0002091 1.00 52.69253 39.72040 32517623 0.248715 0.0020415 44543039 99.98903 100 34070517 88.79 54150809 NA NA NA NA NA NA
AnswerALS CASE_NEUYJ705VN9 122863974 178270837 178270837 122863974 100 61425993 0.0001050 0.98 44.63852 38.44930 34275732 0.324227 0.0022001 55406863 99.99024 100 37266516 85.92 54518769 NA NA NA NA NA NA
AnswerALS CASE_NEUYK029WUU 89122275 114077752 114077752 89122275 100 44558477 0.0000914 0.97 61.38720 46.04638 26265846 0.185776 0.0024906 24955477 99.99403 100 28032018 90.95 41147531 NA NA NA NA NA NA
AnswerALS CASE_NEUYL008GM4 111596389 136189939 136189939 111596389 100 55793552 0.0001722 0.97 68.59611 32.41083 22071962 0.135216 0.0028679 24593550 99.99168 100 22785219 92.39 52394355 NA NA NA NA NA NA
AnswerALS CASE_NEUYL149PRF 108007117 135498385 135498385 108007117 100 54000728 0.0002878 0.98 61.14424 53.84660 36482547 0.206587 0.0025245 27491268 99.99476 100 38738756 91.11 50062588 NA NA NA NA NA NA
AnswerALS CASE_NEUYP226CPW 140904052 200107332 200107332 140904052 100 70445538 0.0001431 1.02 45.97181 39.80486 39830197 0.319377 0.0018772 59203280 99.99079 100 43697397 86.71 62985933 NA NA NA NA NA NA
AnswerALS CASE_NEUYP235ZLD 112041837 154018964 154018964 112041837 100 56012285 0.0006468 0.98 53.34704 30.31082 23345849 0.236692 0.0022270 41977127 99.98459 100 24774214 88.37 50797298 NA NA NA NA NA NA
AnswerALS CASE_NEUYT193FFG 135937514 167443145 167443145 135937514 100 67965213 0.0002058 0.99 55.17711 45.26622 37899750 0.298018 0.0020057 31505631 99.99479 100 40441406 91.04 62909433 NA NA NA NA NA NA
AnswerALS CASE_NEUYY225MNZ 86663158 113081381 113081381 86663158 100 43329287 0.0000491 0.97 61.57635 43.19503 24424016 0.168417 0.0025204 26418223 99.99471 100 25706055 91.35 40143805 NA NA NA NA NA NA
AnswerALS CASE_NEUYY614DN8 143420041 207828429 207828429 143420041 100 71705432 0.0001386 0.98 43.48929 38.17697 39674516 0.341201 0.0021712 64408388 99.99360 100 44205920 85.74 63160903 NA NA NA NA NA NA
AnswerALS CASE_NEUYY878JGP 133161137 172765129 172765129 133161137 100 66576125 0.0004581 0.99 54.69875 45.73749 39512171 0.264335 0.0020122 39603992 99.99333 100 41230805 90.43 61407501 NA NA NA NA NA NA
AnswerALS CASE_NEUZD231YZ6 114115577 160409162 160409162 114115577 100 57054121 0.0003026 0.98 37.42191 39.14512 31398709 0.450324 0.0020169 46293585 99.99357 100 35064123 87.49 50905501 NA NA NA NA NA NA
AnswerALS CASE_NEUZE432DZM 130181306 183450507 183450507 130181306 100 65085949 0.0000718 0.98 46.85383 39.45448 36192628 0.311264 0.0019646 53269201 99.99277 100 40115753 87.01 57917361 NA NA NA NA NA NA
AnswerALS CASE_NEUZF321EW4 137296801 237074262 237074262 137296801 100 68645200 0.0004753 1.01 35.69136 28.75297 34084476 0.352639 0.0019988 99777461 99.99534 100 38615057 83.54 58499666 NA NA NA NA NA NA
AnswerALS CASE_NEUZF473UEP 115673202 160994953 160994953 115673202 100 57829951 0.0005352 0.98 47.71084 36.89973 29707207 0.306990 0.0021394 45321751 99.98850 100 33058534 86.18 51678195 NA NA NA NA NA NA
AnswerALS CASE_NEUZJ053JGZ 133079937 177519663 177519663 133079937 100 66536354 0.0003317 1.00 49.27551 37.35663 33159728 0.317630 0.0020517 44439726 99.99457 100 36138181 88.41 59979953 NA NA NA NA NA NA
AnswerALS CASE_NEUZK054DP5 120214668 154653148 154653148 120214668 100 60103402 0.0004124 1.04 52.53178 45.78244 35404472 0.298436 0.0018783 34438480 99.99346 100 38496742 89.95 54950104 NA NA NA NA NA NA
AnswerALS CASE_NEUZN836GME 145980665 199472112 199472112 145980665 100 72983931 0.0002882 1.01 52.13303 42.78780 42678756 0.260984 0.0020023 53491447 99.99123 100 44497522 89.27 66523707 NA NA NA NA NA NA
AnswerALS CASE_NEUZN936HJ9 81372630 106601993 106601993 81372630 100 40681058 0.0003806 1.00 55.49972 40.91089 21809049 0.244893 0.0018392 25229363 99.98708 100 23946737 86.35 37033610 NA NA NA NA NA NA
AnswerALS CASE_NEUZP278MR4 131323891 176068176 176068176 131323891 100 65655018 0.0006721 1.01 51.81335 37.00994 32585406 0.279093 0.0019754 44744285 99.98945 100 35651501 88.06 59272066 NA NA NA NA NA NA
AnswerALS CASE_NEUZT557DHF 106461904 143299163 143299163 106461904 100 53227723 0.0003853 0.97 58.32994 40.20927 28811446 0.184961 0.0026631 36837259 99.99393 100 30130126 90.24 48805126 NA NA NA NA NA NA
AnswerALS CASE_NEUZT902WVB 148124441 182236026 182236026 148124441 100 74058202 0.0000503 0.98 57.46045 43.65235 39777357 0.269224 0.0021408 34111585 99.99457 100 42140814 91.69 68930822 NA NA NA NA NA NA
AnswerALS CASE_NEUZV656DD1 148595712 191967771 191967771 148595712 100 74290018 0.0002922 1.01 53.56322 40.64046 39012951 0.283583 0.0019968 43372059 99.98945 100 42775759 89.23 67818461 NA NA NA NA NA NA
AnswerALS CASE_NEUZW701NNF 103881710 161910752 161910752 103881710 100 51938334 0.0004089 0.99 38.59967 33.83292 27390995 0.370488 0.0018256 58029042 99.99515 100 31808231 84.18 44505268 NA NA NA NA NA NA
AnswerALS CASE_NEUZX521TKK 98509768 147866623 147866623 98509768 100 49251743 0.0011162 0.99 49.59044 37.31938 27593127 0.221318 0.0025534 49356855 99.99362 100 30499773 86.53 43500814 NA NA NA NA NA NA
AnswerALS CASE_NEUZX847VWV 119842527 151675489 151675489 119842527 100 59914634 0.0005850 0.99 57.32521 42.14669 31967012 0.249421 0.0019800 31832962 99.98894 100 34686632 89.97 55085136 NA NA NA NA NA NA
AnswerALS CASE_NEUZY128BJ2 150783455 204326818 204326818 150783455 100 75386092 0.0001938 0.96 48.60244 37.88189 38704461 0.315447 0.0020149 53543363 99.99253 100 42610444 88.01 67775270 NA NA NA NA NA NA
AnswerALS CASE_NEUZY975XKL 109304246 144951033 144951033 109304246 100 54649315 0.0001080 1.02 50.04858 47.28401 34271213 0.310375 0.0018150 35646787 99.99486 100 38548384 88.36 48940600 NA NA NA NA NA NA
AnswerALS CTRL_NEUAA485DZL 142730071 206651342 206651342 142730071 100 71358075 0.0001363 1.01 42.96172 40.46539 41815801 0.350993 0.0019086 63921271 99.99025 100 46974414 85.30 62633765 NA NA NA NA NA NA
AnswerALS CTRL_NEUAJ025JC3 95976943 127242318 127242318 95976943 100 47985999 0.0002535 0.98 59.67276 40.91501 26031923 0.178385 0.0026401 31265375 99.99485 100 27673100 90.71 44173605 NA NA NA NA NA NA
AnswerALS CTRL_NEUAJ928PAA 119849155 148067308 148067308 119849155 100 59920487 0.0000620 0.98 63.17580 50.11523 37104650 0.193182 0.0026209 28218153 99.99317 100 39200380 91.47 55771640 NA NA NA NA NA NA
AnswerALS CTRL_NEUCA748GF2 107664405 137518200 137518200 107664405 100 53827862 0.0002251 0.98 57.66832 32.94083 22651817 0.238273 0.0020644 29853795 99.99194 100 24571396 89.73 49288757 NA NA NA NA NA NA
AnswerALS CTRL_NEUCV136DHM 133777770 169397330 169397330 133777770 100 66882436 0.0000651 0.99 55.08695 48.92659 41444984 0.278311 0.0018345 35619560 99.99036 100 45549599 89.72 61182809 NA NA NA NA NA NA
AnswerALS CTRL_NEUCV809LL4 75164929 112702935 112702935 75164929 100 37579947 0.0003591 0.99 51.05006 34.10042 19217322 0.199274 0.0029202 37538006 99.99330 100 20568369 87.18 33519005 NA NA NA NA NA NA
AnswerALS CTRL_NEUDA782GW3 84711501 107695370 107695370 84711501 100 42353186 0.0000815 1.00 63.74855 38.74052 20862147 0.160241 0.0026666 22983869 99.99395 100 21427666 91.81 39438521 NA NA NA NA NA NA
AnswerALS CTRL_NEUDE949BP3 106950527 160325830 160325830 106950527 100 53472417 0.0004657 0.97 50.28890 37.22890 29845269 0.213953 0.0025578 53375303 99.99468 100 31526501 88.57 48108748 NA NA NA NA NA NA
AnswerALS CTRL_NEUDM126GNG 109647418 144319019 144319019 109647418 100 54820128 0.0000840 0.98 59.50635 44.56285 32158364 0.185721 0.0027073 34671601 99.99347 100 34382218 89.76 50168400 NA NA NA NA NA NA
AnswerALS CTRL_NEUDT762KUL 104193773 168014070 168014070 104193773 100 52094773 0.0003644 1.00 39.04926 32.66405 27441220 0.338047 0.0021123 63820297 99.99594 100 30288348 85.30 45243066 NA NA NA NA NA NA
AnswerALS CTRL_NEUEB210XRC 126699869 166317212 166317212 126699869 100 63340865 0.0003199 1.00 48.59671 45.47978 37826434 0.338585 0.0019693 39617343 99.98568 100 42145092 87.81 57006910 NA NA NA NA NA NA
AnswerALS CTRL_NEUEY565NWT 99688142 135142105 135142105 99688142 100 49840653 0.0002137 1.00 58.78130 40.86577 27615249 0.170502 0.0026984 35453963 99.99314 100 29065895 90.01 45685875 NA NA NA NA NA NA
AnswerALS CTRL_NEUFL733GX5 123100513 163533801 163533801 123100513 100 61545257 0.0002462 1.02 55.30460 38.73854 31677879 0.236233 0.0020375 40433288 99.99188 100 32733496 90.31 56609176 NA NA NA NA NA NA
AnswerALS CTRL_NEUFZ500KDB 105364734 144983815 144983815 105364734 100 52678661 0.0001249 0.99 56.25394 40.86537 29626090 0.192852 0.0028539 39619081 99.99297 100 31637441 89.34 47960440 NA NA NA NA NA NA
AnswerALS CTRL_NEUFZ508VBV 92018121 113000997 113000997 92018121 100 46006716 0.0000357 1.01 64.99242 44.63934 25222765 0.175065 0.0025146 20982876 99.99490 100 26953022 92.14 42988984 NA NA NA NA NA NA
AnswerALS CTRL_NEUHE723FGT 125537737 162056376 162056376 125537737 100 62764270 0.0011938 0.98 58.65879 32.97615 26721907 0.215906 0.0021614 36518639 99.99267 100 26793823 90.97 58252831 NA NA NA NA NA NA
AnswerALS CTRL_NEUHZ716BZ2 85710543 111187686 111187686 85710543 100 42852487 0.0002070 0.96 61.79334 39.97116 22222904 0.169172 0.0028450 25477143 99.99350 100 23292684 90.31 39527760 NA NA NA NA NA NA
AnswerALS CTRL_NEUJH290RH7 82173096 118342717 118342717 82173096 100 41084532 0.0001731 0.99 54.19480 36.11641 21371505 0.186395 0.0025146 36169621 99.99509 100 23245087 88.94 37082361 NA NA NA NA NA NA
AnswerALS CTRL_NEUJX341NDP 86296043 112040549 112040549 86296043 100 43145527 0.0001699 0.95 61.72160 36.76733 20598281 0.169698 0.0026220 25744506 99.99422 100 21891892 90.82 39861968 NA NA NA NA NA NA
AnswerALS CTRL_NEUKW131XJ2 95809608 136890063 136890063 95809608 100 47902177 0.0004480 0.97 52.02433 41.41099 28345282 0.226584 0.0025512 41080455 99.99452 100 30623541 88.47 43164946 NA NA NA NA NA NA
AnswerALS CTRL_NEULL933JXY 110585326 143995298 143995298 110585326 100 55288588 0.0000544 0.99 55.48995 40.87436 29430905 0.252399 0.0018215 33409972 99.99263 100 32283777 89.42 50400099 NA NA NA NA NA NA
AnswerALS CTRL_NEUMA002VLD 135552971 169095441 169095441 135552971 100 67772754 0.0000385 0.98 53.41844 46.03283 38922106 0.310142 0.0020246 33542470 99.99449 100 41089506 91.08 62765223 NA NA NA NA NA NA
AnswerALS CTRL_NEUMF089KLV 117156561 165059662 165059662 117156561 100 58566711 0.0001651 0.98 44.88286 38.14853 31490598 0.341550 0.0020028 47903101 99.98025 100 35167692 85.93 52245074 NA NA NA NA NA NA
AnswerALS CTRL_NEUML507PFJ 112923055 150315261 150315261 112923055 100 56449107 0.0001161 1.02 43.60568 44.67974 33588188 0.396560 0.0020184 37392206 99.97800 100 37457697 87.15 51219941 NA NA NA NA NA NA
AnswerALS CTRL_NEUMN061ATZ 93524847 128173953 128173953 93524847 100 46759563 0.0001344 0.99 57.80673 45.27378 29016282 0.175560 0.0027322 34649106 99.99388 100 29752572 90.24 43033290 NA NA NA NA NA NA
AnswerALS CTRL_NEUMT184NWC 136862206 224271425 224271425 136862206 100 68422512 0.0025125 0.99 39.43972 32.22339 36139122 0.321582 0.0021129 87409219 99.98745 100 41155454 82.33 58323568 NA NA NA NA NA NA
AnswerALS CTRL_NEUNC876ZB2 118137032 152219678 152219678 118137032 100 59063901 0.0001150 1.00 52.67947 45.68107 34770809 0.295167 0.0018412 34082646 99.99219 100 38077080 88.79 53739361 NA NA NA NA NA NA
AnswerALS CTRL_NEUNN472ACB 115095631 163191184 163191184 115095631 100 57541164 0.0002525 1.01 45.84206 40.27677 32868036 0.322258 0.0022235 48095553 99.98844 100 37297185 86.51 50810753 NA NA NA NA NA NA
AnswerALS CTRL_NEUNW343RXP 81656013 101975419 101975419 81656013 100 40825164 0.0000734 0.99 63.94251 45.41374 23157025 0.172710 0.0026231 20319406 99.99304 100 24466778 91.80 38038971 NA NA NA NA NA NA
AnswerALS CTRL_NEUPH301NNX 97626796 124778743 124778743 97626796 100 48810411 0.0007084 0.98 62.90073 38.68959 24139662 0.168067 0.0026556 27151947 99.99388 100 25335234 91.23 45245936 NA NA NA NA NA NA
AnswerALS CTRL_NEUPL878MTL 119315528 145479308 145479308 119315528 100 59652672 0.0001063 1.01 59.15472 45.27052 32932752 0.255547 0.0018693 26163780 99.99146 100 35298095 91.07 55420022 NA NA NA NA NA NA
AnswerALS CTRL_NEUPW536ZKZ 140584593 183287662 183287662 140584593 100 70282990 0.0000454 1.00 47.46122 45.68001 41869158 0.357446 0.0019376 42703069 99.98676 100 47060687 88.27 63578832 NA NA NA NA NA NA
AnswerALS CTRL_NEURJ861MMD 126644009 177617449 177617449 126644009 100 63318324 0.0001233 0.99 54.49429 33.77473 29996606 0.204296 0.0026134 50973440 99.99419 100 32347065 88.58 57183408 NA NA NA NA NA NA
AnswerALS CTRL_NEURV546WMW 157220261 202295873 202295873 157220261 100 78604322 0.0002336 1.01 53.00219 40.20670 40671295 0.293329 0.0021206 45075612 99.99261 100 42355896 90.81 72498559 NA NA NA NA NA NA
AnswerALS CTRL_NEUUV825HYF 83800552 107396217 107396217 83800552 100 41897686 0.0004498 0.96 63.56130 37.26202 20010218 0.157226 0.0026666 23595665 99.99382 100 20854070 91.47 38901768 NA NA NA NA NA NA
AnswerALS CTRL_NEUVZ050YX7 92660498 126950374 126950374 92660498 100 46327705 0.0003695 0.96 58.44763 35.38709 22463170 0.166282 0.0026063 34289876 99.99451 100 23548444 89.93 42302176 NA NA NA NA NA NA
AnswerALS CTRL_NEUWN092BVG 124441297 267096673 267096673 124441297 100 62217948 0.0007366 1.02 26.44413 22.36445 29868384 0.399273 0.0018759 142655376 99.99566 100 35643330 77.13 49313107 NA NA NA NA NA NA
AnswerALS CTRL_NEUWT164JRQ 135918939 165861184 165861184 135918939 100 67954059 0.0006845 0.99 60.66825 36.63712 30385906 0.236310 0.0021812 29942245 99.99204 100 31316871 92.30 63842878 NA NA NA NA NA NA
AnswerALS CTRL_NEUXC258VTR 152107663 209900868 209900868 152107663 100 76050099 0.0001636 1.00 47.44388 37.26139 39107873 0.318962 0.0022160 57793205 99.99509 100 42315109 88.66 68669786 NA NA NA NA NA NA
AnswerALS CTRL_NEUXP955XW7 114681956 149912733 149912733 114681956 100 57335068 0.0001184 1.01 52.71462 39.41866 29550314 0.283886 0.0018471 35230777 99.98969 100 32850947 88.44 51944509 NA NA NA NA NA NA
AnswerALS CTRL_NEUXW311EFC 104639552 288942845 288942845 104639552 100 52317273 0.0001632 1.02 18.01321 13.99294 20216523 0.464670 0.0020450 184303293 99.99522 100 25421145 69.72 37720814 NA NA NA NA NA NA
AnswerALS CTRL_NEUYM205MRL 107448896 130702708 130702708 107448896 100 53721197 0.0001384 0.98 66.54306 44.21693 28898107 0.163942 0.0026897 23253812 99.99395 100 30061334 92.29 50334794 NA NA NA NA NA NA
neurolincs.diMN 00072001A02 135941676 230048169 230048169 135941676 100 67891519 0.0000486 1.00 38.23806 NA NA 0.322099 0.0044128 94106493 99.88330 NA NA 85.10 59399312 NA NA NA NA NA NA
neurolincs.diMN 00072001B02 94178800 113979200 113979200 94178800 100 47033246 0.0002407 1.04 58.12804 NA NA 0.270977 0.0041548 19800400 99.88075 NA NA 91.78 44306370 NA NA NA NA NA NA
neurolincs.diMN 00072002A02 128354706 233021285 233021285 128354706 100 64131194 0.0000189 1.05 32.35120 NA NA 0.385579 0.0035951 104666579 99.92808 NA NA 81.85 54374177 NA NA NA NA NA NA
neurolincs.diMN 00072002B02 121345546 178706446 178706446 121345546 100 60617500 0.0000132 1.03 43.85413 NA NA 0.325116 0.0033535 57360900 99.90890 NA NA 83.17 54504534 NA NA NA NA NA NA
neurolincs.diMN 00072006A01 127718938 173144213 173144213 127718938 100 63815376 0.0001075 1.08 48.64651 NA NA 0.314414 0.0034966 45425275 99.93095 NA NA 89.19 58172615 NA NA NA NA NA NA
neurolincs.diMN 00072006B01 126436139 163172628 163172628 126436139 100 63166742 0.0000985 1.04 52.35554 NA NA 0.298745 0.0032790 36736489 99.91881 NA NA 89.75 58149679 NA NA NA NA NA NA
neurolincs.diMN 00072007A01 125824321 159464428 159464428 125824321 100 62865712 0.0000072 1.09 52.17988 NA NA 0.313698 0.0036019 33640107 99.92617 NA NA 90.13 58022536 NA NA NA NA NA NA
neurolincs.diMN 00072007B01 140248486 185851687 185851687 140248486 100 70064449 0.0000110 1.02 49.51831 NA NA 0.317949 0.0033093 45603201 99.91473 NA NA 88.78 64085726 NA NA NA NA NA NA
neurolincs.diMN 00072008A02 113439206 174996013 174996013 113439206 100 56644047 0.0001302 1.00 44.07174 NA NA 0.287272 0.0049033 61556807 99.86679 NA NA 86.51 50470377 NA NA NA NA NA NA
neurolincs.diMN 00072008B02 130419423 186533158 186533158 130419423 100 65118457 0.0001133 1.02 48.09248 NA NA 0.282421 0.0047360 56113735 99.86006 NA NA 88.34 59327132 NA NA NA NA NA NA
neurolincs.diMN 00072010A02 97616064 123704269 123704269 97616064 100 48751803 0.0002113 1.02 56.76044 NA NA 0.253716 0.0043931 26088205 99.88480 NA NA 90.40 45386503 NA NA NA NA NA NA
neurolincs.diMN 00072010B02 97718802 128795458 128795458 97718802 100 48795660 0.0002677 1.02 53.05946 NA NA 0.271663 0.0043221 31076656 99.86954 NA NA 89.62 45162304 NA NA NA NA NA NA
neurolincs.diMN 00072012A01 148024478 221266815 221266815 148024478 100 73944529 0.0000147 1.06 41.98420 NA NA 0.345136 0.0035806 73242337 99.90852 NA NA 85.59 65569118 NA NA NA NA NA NA
neurolincs.diMN 00072012B01 122573980 213140649 213140649 122573980 100 61231109 0.0000237 1.09 34.86024 NA NA 0.363857 0.0034863 90566669 99.90882 NA NA 82.91 52372164 NA NA NA NA NA NA
neurolincs.diMN 00072013A02 118696846 192328501 192328501 118696846 100 59305314 0.0000342 1.07 38.34418 NA NA 0.350213 0.0035889 73631655 99.92736 NA NA 85.32 51716157 NA NA NA NA NA NA
neurolincs.diMN 00072013B02 46670716 59683321 59683321 46670716 100 23314228 0.0000345 1.02 56.50135 NA NA 0.246293 0.0037340 13012605 99.90945 NA NA 90.82 21658777 NA NA NA NA NA NA
neurolincs.diMN 00072014A02 126791091 241860665 241860665 126791091 100 63323993 0.0000448 0.97 32.89437 NA NA 0.338306 0.0042676 115069574 99.88713 NA NA 82.07 53450807 NA NA NA NA NA NA
neurolincs.diMN 00072014B02 128538219 181437080 181437080 128538219 100 64204227 0.0000319 1.02 48.77057 NA NA 0.282723 0.0038709 52898861 99.89905 NA NA 89.19 58677514 NA NA NA NA NA NA
neurolincs.diMN 00072015A01 115356666 158112293 158112293 115356666 100 57615661 0.0001570 1.04 48.97028 NA NA 0.300918 0.0039417 42755627 99.89134 NA NA 88.68 52283322 NA NA NA NA NA NA
neurolincs.diMN 00072015B01 126695445 219773032 219773032 126695445 100 63292889 0.0006390 1.05 35.27499 NA NA 0.357848 0.0034305 93077587 99.91344 NA NA 83.83 54369447 NA NA NA NA NA NA
neurolincs.diMN 00072018A02 111320345 138933136 138933136 111320345 100 55562883 0.0001702 1.06 54.60476 NA NA 0.291659 0.0040284 27612791 99.82521 NA NA 88.21 51515998 NA NA NA NA NA NA
neurolincs.diMN 00072018B02 132755451 180480035 180480035 132755451 100 66288152 0.0001320 1.01 49.23297 NA NA 0.304696 0.0040931 47724584 99.86505 NA NA 88.72 60940845 NA NA NA NA NA NA
neurolincs.diMN 00072019A02 124986603 236421103 236421103 124986603 100 62440538 0.0001764 1.02 32.79879 NA NA 0.347422 0.0038855 111434500 99.91557 NA NA 82.54 52805605 NA NA NA NA NA NA
neurolincs.diMN 00072019B02 147282515 183896260 183896260 147282515 100 73550040 0.0001682 0.98 53.82492 NA NA 0.303372 0.0040621 36613745 99.87613 NA NA 90.94 68691397 NA NA NA NA NA NA
neurolincs.diMN 00072028A01 132870476 220521382 220521382 132870476 100 66373545 0.0001004 1.07 37.28181 NA NA 0.351354 0.0036057 87650906 99.90714 NA NA 82.84 57550940 NA NA NA NA NA NA
neurolincs.diMN 00072028B01 128995074 193530490 193530490 128995074 100 64452299 0.0001071 1.06 41.89889 NA NA 0.343485 0.0031821 64535416 99.92986 NA NA 85.95 57436868 NA NA NA NA NA NA
neurolincs.diMN 00072029A01 106521084 182347069 182347069 106521084 100 53202122 0.0003117 1.06 36.33133 NA NA 0.346029 0.0039574 75825985 99.89031 NA NA 83.28 45652536 NA NA NA NA NA NA
neurolincs.diMN 00072029B01 129663114 155124570 155124570 129663114 100 64781383 0.0000279 1.10 55.16994 NA NA 0.316344 0.0031647 25461456 99.92261 NA NA 90.69 60478486 NA NA NA NA NA NA
neurolincs.diMN 00072034A01 126821822 169942398 169942398 126821822 100 63361107 0.0000734 1.05 49.69402 NA NA 0.307243 0.0036640 43120576 99.92146 NA NA 88.71 58025659 NA NA NA NA NA NA
neurolincs.diMN 00072034C01 136723117 187549403 187549403 136723117 100 68306236 0.0001140 1.04 45.57472 NA NA 0.349683 0.0032756 50826286 99.91907 NA NA 87.16 62019587 NA NA NA NA NA NA
neurolincs.diMN A-042-00iCTR-003 72933637 115482294 115482294 72933637 100 36430618 0.0000614 1.03 48.36477 NA NA 0.196205 0.0021612 42548657 99.90073 NA NA 86.39 32117381 NA NA NA NA NA NA
neurolincs.diMN A-042-00iCTR-004 80664165 114902116 114902116 80664165 100 40291268 0.0000522 1.06 53.36115 NA NA 0.205768 0.0019302 34237951 99.89880 NA NA 87.58 36178657 NA NA NA NA NA NA
neurolincs.diMN A-042-25iCTR-003 90791001 196170471 196170471 90791001 100 45356754 0.0001678 1.04 29.61257 NA NA 0.321581 0.0020212 105379470 99.91465 NA NA 76.83 35959903 NA NA NA NA NA NA
neurolincs.diMN A-042-25iCTR-004 105034279 152195347 152195347 105034279 100 52463612 0.0000295 1.08 50.06550 NA NA 0.243061 0.0017331 47161068 99.89808 NA NA 85.75 46397163 NA NA NA NA NA NA
neurolincs.diMN A-042-28iALS-003 60575786 85175631 85175631 60575786 100 30261072 0.0000304 1.00 56.65664 NA NA 0.169235 0.0019201 24599845 99.91145 NA NA 89.22 27509794 NA NA NA NA NA NA
neurolincs.diMN A-042-28iALS-005 85676346 138127203 138127203 85676346 100 42771822 0.0000311 1.02 46.50457 NA NA 0.215862 0.0017702 52450857 99.84511 NA NA 85.96 37588074 NA NA NA NA NA NA
neurolincs.diMN A-042-29iALS-003 87345844 104514733 104514733 87345844 100 43633538 0.0000234 1.03 62.47783 NA NA 0.228698 0.0018449 17168889 99.90982 NA NA 90.52 40374838 NA NA NA NA NA NA
neurolincs.diMN A-042-29iALS-004 95816596 141144444 141144444 95816596 100 47865904 0.0000585 1.05 48.69636 NA NA 0.251449 0.0017006 45327848 99.91151 NA NA 86.92 42550998 NA NA NA NA NA NA
neurolincs.diMN A-042-30iALS-003 77416918 102396365 102396365 77416918 100 38671139 0.0000805 1.04 58.61526 NA NA 0.194683 0.0019603 24979447 99.90359 NA NA 88.96 35212928 NA NA NA NA NA NA
neurolincs.diMN A-042-30iALS-004 102751248 136491201 136491201 102751248 100 51326745 0.0000490 1.07 58.26979 NA NA 0.197065 0.0017537 33739953 99.90486 NA NA 89.08 46825808 NA NA NA NA NA NA
neurolincs.diMN A-042-52iALS-003 73314114 105152444 105152444 73314114 100 36626533 0.0000241 1.02 49.57568 NA NA 0.256968 0.0018323 31838330 99.91673 NA NA 87.63 32786448 NA NA NA NA NA NA
neurolincs.diMN A-042-52iALS-004 95698993 133431493 133431493 95698993 100 47804764 0.0000155 1.07 50.82951 NA NA 0.262022 0.0016450 37732500 99.90651 NA NA 87.51 43059847 NA NA NA NA NA NA
neurolincs.diMN A-042-83iCTR-003 95760241 243258163 243258163 95760241 100 47840562 0.0000123 1.08 22.95447 NA NA 0.376408 0.0020284 147497922 99.91738 NA NA 71.68 35437258 NA NA NA NA NA NA
neurolincs.diMN A-042-83iCTR-004 84808205 166729922 166729922 84808205 100 42367425 0.0000080 1.09 33.60215 NA NA 0.301175 0.0017554 81921717 99.91350 NA NA 79.32 34527944 NA NA NA NA NA NA
catanese c9orf72_1 75957394 81967185 81967185 75957394 100 37968138 0.0000180 1.08 61.65157 NA NA 0.315076 0.0025560 6009791 99.97220 NA NA 95.02 36788530 NA NA NA NA NA NA
catanese c9orf72_2 72919132 78480260 78480260 72919132 100 36451110 0.0000282 1.05 62.35228 NA NA 0.309170 0.0026208 5561128 99.97681 NA NA 95.08 35311214 NA NA NA NA NA NA
catanese c9orf72_3 76337728 82563723 82563723 76337728 100 38161015 0.0000060 1.06 58.64808 NA NA 0.346512 0.0027519 6225995 99.97944 NA NA 94.71 36947989 NA NA NA NA NA NA
catanese c9orf72_4 71229641 76888537 76888537 71229641 100 35607323 0.0000226 1.10 60.84190 NA NA 0.323337 0.0025268 5658896 99.97895 NA NA 94.78 34466646 NA NA NA NA NA NA
catanese c9orf72_5 70109568 76105593 76105593 70109568 100 35046568 0.0000163 1.09 56.96976 NA NA 0.362158 0.0026023 5996025 99.97656 NA NA 94.61 33883013 NA NA NA NA NA NA
catanese c9orf72_6 69814167 75301066 75301066 69814167 100 34898923 0.0000098 1.11 57.44992 NA NA 0.361781 0.0026903 5486899 99.97662 NA NA 94.95 33801000 NA NA NA NA NA NA
catanese ctrl_1 65434941 70580531 70580531 65434941 100 32708636 0.0000245 1.08 59.90526 NA NA 0.334629 0.0025768 5145590 99.97300 NA NA 95.09 31699462 NA NA NA NA NA NA
catanese ctrl_2 60047749 64571298 64571298 60047749 100 30017201 0.0000076 1.06 62.14138 NA NA 0.312248 0.0023685 4523549 99.97777 NA NA 95.42 29103408 NA NA NA NA NA NA
catanese ctrl_3 63620482 68216444 68216444 63620482 100 31804721 0.0000107 1.08 59.72607 NA NA 0.341274 0.0024669 4595962 99.98265 NA NA 95.50 30862009 NA NA NA NA NA NA
catanese fus_1 67955571 73428734 73428734 67955571 100 33970617 0.0000100 1.06 60.63928 NA NA 0.325379 0.0025217 5473163 99.97890 NA NA 95.00 32894443 NA NA NA NA NA NA
catanese fus_2 63220005 68675328 68675328 63220005 100 31603980 0.0000072 1.07 60.85049 NA NA 0.319067 0.0025170 5455323 99.98095 NA NA 95.21 30591145 NA NA NA NA NA NA
catanese fus_3 74148845 79882326 79882326 74148845 100 37066760 0.0000092 1.05 57.39093 NA NA 0.363480 0.0025698 5733481 99.97933 NA NA 95.30 35918835 NA NA NA NA NA NA
catanese fus_4 59851095 64881696 64881696 59851095 100 29921067 0.0000190 1.07 61.06491 NA NA 0.318017 0.0025564 5030601 99.98503 NA NA 95.41 28970978 NA NA NA NA NA NA
catanese fus_5 70100137 75733720 75733720 70100137 100 35043505 0.0000162 1.06 55.75257 NA NA 0.379645 0.0024940 5633583 99.98127 NA NA 95.09 33946048 NA NA NA NA NA NA
catanese fus_6 66401477 72139932 72139932 66401477 100 33195335 0.0000102 1.08 58.00465 NA NA 0.350565 0.0025423 5738455 99.98372 NA NA 94.95 32122277 NA NA NA NA NA NA
catanese iso_1 65420693 70669639 70669639 65420693 100 32703372 0.0000000 1.06 60.57990 NA NA 0.326263 0.0027316 5248946 99.97868 NA NA 95.13 31687063 NA NA NA NA NA NA
catanese iso_2 72233630 78605662 78605662 72233630 100 36107695 0.0000000 1.05 58.27189 NA NA 0.346863 0.0024793 6372032 99.97475 NA NA 95.10 34960517 NA NA NA NA NA NA
catanese iso_3 70716047 76451317 76451317 70716047 100 35350396 0.0000065 1.04 61.47153 NA NA 0.316114 0.0024646 5735270 99.97843 NA NA 95.15 34278261 NA NA NA NA NA NA
dafinca c9orf72_1 121035567 132747772 132747772 121035567 100 60511122 0.0000018 1.19 58.86387 NA NA 0.331559 0.0026354 11712205 99.98899 NA NA 92.58 57798843 NA NA NA NA NA NA
dafinca c9orf72_2 118789660 132869385 132869385 118789660 100 59388555 0.0000038 1.31 65.47521 NA NA 0.238722 0.0023471 14079725 99.98944 NA NA 91.76 56299561 NA NA NA NA NA NA
dafinca c9orf72_3 101537136 109650109 109650109 101537136 100 50761452 0.0000000 1.14 65.64582 NA NA 0.265317 0.0024822 8112973 99.98598 NA NA 91.22 48515807 NA NA NA NA NA NA
dafinca c9orf72_4 106049359 119503299 119503299 106049359 100 53018709 0.0000000 1.21 62.38078 NA NA 0.269820 0.0024909 13453940 99.98874 NA NA 92.11 50254110 NA NA NA NA NA NA
dafinca ctrl_1 105491420 119502002 119502002 105491420 100 52737233 0.0000021 1.22 67.63313 NA NA 0.203468 0.0027350 14010582 99.98393 NA NA 91.40 50043374 NA NA NA NA NA NA
dafinca iso_1 110514258 126081076 126081076 110514258 100 55250944 0.0000020 1.14 58.38462 NA NA 0.305962 0.0025204 15566818 99.98881 NA NA 89.66 51904662 NA NA NA NA NA NA
dafinca iso_2 106736217 117587500 117587500 106736217 100 53359671 0.0000000 1.16 59.85868 NA NA 0.315709 0.0026161 10851283 99.98419 NA NA 90.48 50824778 NA NA NA NA NA NA
dafinca iso_3 106149403 119518192 119518192 106149403 100 53067334 0.0000063 1.19 67.64927 NA NA 0.208851 0.0026364 13368789 99.98612 NA NA 90.97 50439866 NA NA NA NA NA NA
dafinca iso_4 92324252 103350221 103350221 92324252 100 46155034 0.0000000 1.18 57.64835 NA NA 0.329921 0.0026080 11025969 99.98464 NA NA 89.83 43738930 NA NA NA NA NA NA
dafinca iso_5 110135429 123636396 123636396 110135429 100 55060726 0.0000000 1.07 50.65312 NA NA 0.408146 0.0024266 13500967 99.98731 NA NA 89.57 51988008 NA NA NA NA NA NA
dafinca iso_6 112546857 126042797 126042797 112546857 100 56265174 0.0000000 1.23 45.18061 NA NA 0.474039 0.0025985 13495940 99.98533 NA NA 89.66 53279237 NA NA NA NA NA NA
dafinca iso_7 94610729 105135911 105135911 94610729 100 47299602 0.0000024 1.23 59.79154 NA NA 0.310400 0.0024351 10525182 99.98782 NA NA 90.88 44856979 NA NA NA NA NA NA
dafinca ctrl_1 16576302 17489968 17489968 16576302 100 8275371 0.0000000 1.08 85.36618 NA NA 0.073477 0.0041740 913666 99.84580 NA NA 96.02 8070745 NA NA NA NA NA NA
dafinca ctrl_2 18972276 20097878 20097878 18972276 100 9472448 0.0000000 1.09 83.99444 NA NA 0.082375 0.0040685 1125602 99.85568 NA NA 95.60 9202716 NA NA NA NA NA NA
dafinca ctrl_3 19783273 20867596 20867596 19783273 100 9878007 0.0000000 1.11 84.84853 NA NA 0.079675 0.0039749 1084323 99.86221 NA NA 96.04 9633247 NA NA NA NA NA NA
dafinca ctrl_4 15583580 16625552 16625552 15583580 100 7776614 0.0000000 1.21 81.17492 NA NA 0.106605 0.0039203 1041972 99.80523 NA NA 91.17 7568676 NA NA NA NA NA NA
dafinca tardbp_1 19574454 20693487 20693487 19574454 100 9772054 0.0000000 1.21 83.90709 NA NA 0.086220 0.0038139 1119033 99.84497 NA NA 94.26 9511682 NA NA NA NA NA NA
dafinca tardbp_2 18517769 19719622 19719622 18517769 100 9239181 0.0000372 1.23 82.91080 NA NA 0.089737 0.0041516 1201853 99.78719 NA NA 93.02 8998264 NA NA NA NA NA NA
dafinca tardbp_3 20485715 21679042 21679042 20485715 100 10224310 0.0000000 1.19 81.68852 NA NA 0.109326 0.0039982 1193327 99.81892 NA NA 93.58 9957003 NA NA NA NA NA NA
dafinca tardbp_4 21895246 23787368 23787368 21895246 100 10932302 0.0000211 1.29 71.93412 NA NA 0.191469 0.0039524 1892122 99.86005 NA NA 93.74 10582849 NA NA NA NA NA NA
dafinca tardbp_5 18544776 19538517 19538517 18544776 100 9258793 0.0000129 1.09 84.43084 NA NA 0.083507 0.0040231 993741 99.85338 NA NA 95.57 9003671 NA NA NA NA NA NA
dafinca tardbp_6 20071514 21044889 21044889 20071514 100 10025089 0.0000118 1.09 85.35948 NA NA 0.080760 0.0036381 973375 99.89370 NA NA 96.13 9778365 NA NA NA NA NA NA
luisier d35_ctrl_1 14137164 17365755 17365755 14137164 100 14137164 0.0000319 0.97 NA NA NA 0.424189 0.0025543 3228591 0.00000 NA NA 89.92 12777849 1.9300484 NA 47 60.00000 35.22582 47
luisier d35_ctrl_2 12395390 15087201 15087201 12395390 100 12395390 0.0000000 0.92 NA NA NA 0.435478 0.0028154 2691811 0.00000 NA NA 90.20 11235044 1.9136214 NA 47 60.00000 36.35613 47
luisier d35_ctrl_3 13781703 16430800 16430800 13781703 100 13781703 0.0000000 0.92 NA NA NA 0.455100 0.0027615 2649097 0.00000 NA NA 90.76 12561469 1.8540827 NA 47 60.00000 37.38918 47
luisier d35_vcp_1 10394568 12882428 12882428 10394568 100 10394568 0.0000135 1.09 NA NA NA 0.446962 0.0024339 2487860 0.00000 NA NA 89.00 9302422 2.0395963 NA 48 60.00000 37.34052 48
luisier d35_vcp_2 15815865 19279401 19279401 15815865 100 15815865 0.0000000 1.00 NA NA NA 0.443607 0.0024008 3463536 0.00000 NA NA 90.36 14356502 2.0067293 NA 48 60.00000 36.71011 48
luisier d35_vcp_3 5906382 7352632 7352632 5906382 100 5906382 0.0000000 0.87 NA NA NA 0.282392 0.0029136 1446250 0.00000 NA NA 90.28 5362641 1.8340739 NA 45 60.00000 22.58967 45
wang iso_1 30043364 31484983 31484983 30043364 100 14914560 0.0000161 1.08 77.98233 NA NA 0.157261 0.0063193 1441619 99.28688 NA NA 90.82 14677818 NA NA NA NA NA NA
wang iso_2 30198322 31651805 31651805 30198322 100 14981698 0.0000641 1.04 78.00677 NA NA 0.156546 0.0065433 1453483 99.22206 NA NA 90.39 14766976 NA NA NA NA NA NA
wang sod1_1 30809361 32337592 32337592 30809361 100 15287653 0.0000315 1.06 78.14520 NA NA 0.153305 0.0065095 1528231 99.24031 NA NA 90.32 15039892 NA NA NA NA NA NA
wang sod1_2 30686515 32213431 32213431 30686515 100 15236081 0.0000159 1.05 78.11696 NA NA 0.154028 0.0062301 1526916 99.30147 NA NA 90.98 14983631 NA NA NA NA NA NA
kiskinis iso_1 12452702 17772558 17772558 12452702 100 6217630 0.0000000 1.23 55.95839 NA NA 0.138765 0.0025517 5319856 99.85993 NA NA 80.22 5657335 NA NA NA NA NA NA
kiskinis iso_2 10126374 14391602 14391602 10126374 100 5057244 0.0000000 1.17 59.25709 NA NA 0.092385 0.0055493 4265228 99.88262 NA NA 57.22 4604554 NA NA NA NA NA NA
kiskinis iso_3 18104053 32559601 32559601 18104053 100 9040767 0.0000000 1.21 41.11135 NA NA 0.188924 0.0029665 14455548 99.87561 NA NA 72.59 7772222 NA NA NA NA NA NA
kiskinis sod1_1 16718799 18243146 18243146 16718799 100 8343800 0.0000747 1.11 36.75684 NA NA 0.579065 0.0036592 1524347 99.81339 NA NA 71.79 8048144 NA NA NA NA NA NA
kiskinis sod1_2 30656110 32740754 32740754 30656110 100 15295018 0.0000000 1.15 39.27142 NA NA 0.563443 0.0020756 2084644 99.78447 NA NA 91.61 14850599 NA NA NA NA NA NA
sareen c9orf72_1 24845406 33212470 33212470 24845406 100 24845406 0.0000101 1.09 NA NA NA 0.493514 0.0028375 8367064 0.00000 NA NA 86.58 21655725 1.7767771 NA 50 50.00000 42.08267 50
sareen c9orf72_2 28151852 37739985 37739985 28151852 100 28151852 0.0000000 1.10 NA NA NA 0.513295 0.0028173 9588133 0.00000 NA NA 86.21 24431401 1.9300992 NA 50 50.00000 43.94880 50
sareen c9orf72_3 41219527 56126483 56126483 41219527 100 41219527 0.0000099 1.07 NA NA NA 0.527217 0.0030292 14906956 0.00000 NA NA 86.16 35777527 1.7798850 NA 50 50.00000 45.31533 50
sareen c9orf72_4 36409834 51259702 51259702 36409834 100 36409834 0.0000035 1.09 NA NA NA 0.556295 0.0027945 14849868 0.00000 NA NA 85.25 31216316 1.7837984 NA 49 50.00000 48.03861 50
sareen ctrl_1 34637930 47037378 47037378 34637930 100 34637930 0.0000113 1.09 NA NA NA 0.515683 0.0031012 12399448 0.00000 NA NA 86.02 29995779 1.7143701 NA 49 50.00000 44.23380 50
sareen ctrl_2 36036948 51713786 51713786 36036948 100 36036948 0.0000040 1.07 NA NA NA 0.529704 0.0030175 15676838 0.00000 NA NA 83.66 30377803 1.8764297 NA 50 50.00000 45.92756 50
sareen ctrl_3 30120447 41597088 41597088 30120447 100 30120447 0.0000000 1.10 NA NA NA 0.527209 0.0028863 11476641 0.00000 NA NA 85.80 26005996 1.7897096 NA 50 50.00000 45.40106 50
sareen ctrl_4 32042851 45335936 45335936 32042851 100 32042851 0.0000000 1.11 NA NA NA 0.564093 0.0028951 13293085 0.00000 NA NA 84.18 27146239 1.8080937 NA 50 50.00000 49.01965 50
sommer c9orf72_1 64336887 68180133 68180133 64336887 100 32164997 0.0000211 1.15 57.56799 NA NA 0.371038 0.0035648 3843246 99.98929 NA NA 95.53 31119676 NA NA NA NA NA NA
sommer c9orf72_2 59830017 63876868 63876868 59830017 100 29911673 0.0000151 1.18 58.66177 NA NA 0.354318 0.0044798 4046851 99.98885 NA NA 95.38 28942710 NA NA NA NA NA NA
sommer c9orf72_3 69515736 74358559 74358559 69515736 100 34754477 0.0000065 1.16 53.89325 NA NA 0.405207 0.0037721 4842823 99.99024 NA NA 95.36 33598568 NA NA NA NA NA NA
sommer c9orf72_4 80391972 86053600 86053600 80391972 100 40188899 0.0000113 1.19 56.87527 NA NA 0.371822 0.0037454 5661628 99.98237 NA NA 95.13 38828950 NA NA NA NA NA NA
sommer c9orf72_5 61652359 65967842 65967842 61652359 100 30821964 0.0000074 1.16 59.42428 NA NA 0.344064 0.0033644 4315483 99.98632 NA NA 95.58 29791587 NA NA NA NA NA NA
sommer c9orf72_6 70120140 75192973 75192973 70120140 100 35054981 0.0000227 1.20 59.53601 NA NA 0.340776 0.0038008 5072833 99.98548 NA NA 95.07 33842839 NA NA NA NA NA NA
sommer ctrl_1 61955188 66357819 66357819 61955188 100 30973008 0.0000256 1.15 60.87844 NA NA 0.326305 0.0055210 4402631 99.98520 NA NA 94.27 29911391 NA NA NA NA NA NA
sommer ctrl_2 70169531 75521771 75521771 70169531 100 35078491 0.0000097 1.13 60.25348 NA NA 0.330383 0.0048517 5352240 99.98212 NA NA 94.38 33866702 NA NA NA NA NA NA
sommer ctrl_3 62797464 67487027 67487027 62797464 100 31393786 0.0000327 1.16 61.94428 NA NA 0.312421 0.0042264 4689563 99.98425 NA NA 95.09 30310132 NA NA NA NA NA NA
sommer ctrl_4 64222789 69085377 69085377 64222789 100 32105084 0.0000282 1.22 55.42455 NA NA 0.383816 0.0037653 4862588 99.98035 NA NA 95.04 30986550 NA NA NA NA NA NA
sommer ctrl_5 62956346 66994033 66994033 62956346 100 31473476 0.0000036 1.21 58.64255 NA NA 0.356663 0.0042383 4037687 99.98508 NA NA 95.39 30464986 NA NA NA NA NA NA
sommer ctrl_6 61029668 64804558 64804558 61029668 100 30511929 0.0000185 1.27 55.20029 NA NA 0.396642 0.0044914 3774890 99.99048 NA NA 95.64 29601506 NA NA NA NA NA NA
sterneckert c9orf72_1 29486569 33917688 33917688 29486569 100 29486569 0.0000120 0.90 NA NA NA 0.579341 0.0027601 4431119 0.00000 NA NA 92.87 27517196 1.9098705 NA 48 76.00000 47.13294 48
sterneckert c9orf72_2 31243868 36606014 36606014 31243868 100 31243868 0.0000038 0.93 NA NA NA 0.577691 0.0028034 5362146 0.00000 NA NA 92.55 29058077 1.7791890 NA 48 76.00000 46.60611 48
sterneckert c9orf72_3 32063553 37667089 37667089 32063553 100 32063553 0.0000148 0.94 NA NA NA 0.588367 0.0027117 5603536 0.00000 NA NA 92.49 29798603 2.0554790 NA 48 76.00000 47.71547 48
sterneckert ctrl_1 33374081 38505971 38505971 33374081 100 33374081 0.0000071 0.89 NA NA NA 0.601435 0.0028147 5131890 0.00000 NA NA 92.91 31164000 2.0262374 NA 47 76.00000 48.85676 48
sterneckert ctrl_2 34261753 40216782 40216782 34261753 100 34261753 0.0000103 0.92 NA NA NA 0.614326 0.0027964 5955029 0.00000 NA NA 92.58 31871446 1.9240435 NA 47 76.00000 49.77593 48
sterneckert ctrl_3 33589817 38967746 38967746 33589817 100 33589817 0.0000140 0.91 NA NA NA 0.610028 0.0028401 5377929 0.00000 NA NA 92.83 31330830 1.6798903 NA 47 76.00000 49.31932 48
kapeli ctrl_1 20435843 25667654 25667654 20435843 100 20435843 0.0000061 0.85 NA NA NA 0.554723 0.0047651 5231811 0.00000 NA NA 87.77 18036576 2.1085959 NA 48 50.00000 22.71533 48
kapeli ctrl_2 30183571 37590329 37590329 30183571 100 30183571 0.0000000 0.86 NA NA NA 0.582816 0.0034462 7406758 0.00000 NA NA 86.97 26825417 1.6451473 NA 47 50.00000 49.82654 47
kapeli ctrl_3 12990116 16093163 16093163 12990116 100 12990116 0.0000000 0.83 NA NA NA 0.455431 0.0066942 3103047 0.00000 NA NA 87.30 11590391 1.6911131 NA 47 50.00000 36.04786 47
kapeli fus_1 11628347 14571553 14571553 11628347 100 11628347 0.0000000 0.89 NA NA NA 0.421617 0.0026919 2943206 0.00000 NA NA 88.79 10382274 1.6719885 NA 47 50.00000 35.60242 47
kapeli fus_2 20542668 26014667 26014667 20542668 100 20542668 0.0000130 0.82 NA NA NA 0.506807 0.0025970 5471999 0.00000 NA NA 88.57 18294585 1.7357264 NA 47 50.00000 43.59158 48
kapeli fus_3 29894560 37829682 37829682 29894560 100 29894560 0.0000089 0.82 NA NA NA 0.567029 0.0027094 7935122 0.00000 NA NA 88.36 26553868 1.6529225 NA 48 50.00000 48.45148 48
desantis ctrl_1 36464752 66855277 66855277 36464752 100 18210429 0.0000810 1.04 38.58190 NA NA 0.251628 0.0022052 30390525 99.87963 NA NA 82.22 15195161 NA NA NA NA NA NA
desantis ctrl_2 40806682 97439508 97439508 40806682 100 20381742 0.0001051 1.01 17.30446 NA NA 0.549032 0.0022554 56632826 99.89414 NA NA 70.47 14822076 NA NA NA NA NA NA
desantis ctrl_3 39635903 75448922 75448922 39635903 100 19795267 0.0001564 1.00 36.44447 NA NA 0.265744 0.0021035 35813019 99.88554 NA NA 81.60 16465064 NA NA NA NA NA NA
desantis fus_1 35612797 66471955 66471955 35612797 100 17785490 0.0000883 0.99 35.21769 NA NA 0.300553 0.0021299 30859158 99.88258 NA NA 79.99 14476588 NA NA NA NA NA NA
desantis fus_2 47294523 107673051 107673051 47294523 100 23619629 0.0000349 1.02 14.42152 NA NA 0.640610 0.0022572 60378528 99.88315 NA NA 72.36 17684239 NA NA NA NA NA NA
desantis fus_3 37794691 71049470 71049470 37794691 100 18874586 0.0000409 1.03 35.62457 NA NA 0.289365 0.0021430 33254779 99.87956 NA NA 81.44 15659611 NA NA NA NA NA NA
smith ctrl_1 56523441 63212608 63212608 56523441 100 28252066 0.0000000 1.14 76.33318 NA NA 0.101840 0.0020922 6689167 99.96584 NA NA 92.92 26581477 NA NA NA NA NA NA
smith ctrl_2 72973159 81543822 81543822 72973159 100 36477011 0.0000033 1.12 75.04343 NA NA 0.119042 0.0019577 8570663 99.97378 NA NA 93.03 34320173 NA NA NA NA NA NA
smith tardbp_1 81164834 89990577 89990577 81164834 100 40567587 0.0000155 1.11 78.09236 NA NA 0.091812 0.0021474 8825743 99.96346 NA NA 93.09 38444351 NA NA NA NA NA NA
smith tardbp_2 81670004 90694956 90694956 81670004 100 40820246 0.0000123 1.12 77.78844 NA NA 0.094052 0.0022170 9024952 99.96386 NA NA 93.10 38679666 NA NA NA NA NA NA
smith tardbp_3 68577024 76199035 76199035 68577024 100 34276814 0.0000219 1.11 78.46129 NA NA 0.085099 0.0020722 7622011 99.96588 NA NA 93.10 32467252 NA NA NA NA NA NA
bhinge iso_1 49358770 62447827 62447827 49358770 100 49358770 0.0000268 1.06 NA NA NA 0.455262 0.0016714 13089057 0.00000 NA NA 89.15 44074145 0.9649444 NA 49 100.00000 15.58140 49
bhinge iso_2 57907498 75011913 75011913 57907498 100 57907498 0.0000169 1.07 NA NA NA 0.493924 0.0016511 17104415 0.00000 NA NA 87.86 50957825 1.0323901 NA 50 100.00000 18.07492 50
bhinge sod1_1 57424532 74874820 74874820 57424532 100 57424532 0.0000593 1.08 NA NA NA 0.467025 0.0016817 17450288 0.00000 NA NA 88.12 50682994 0.9878292 NA 50 100.00000 17.54508 50
bhinge sod1_2 46422296 59960152 59960152 46422296 100 46422296 0.0000103 1.04 NA NA NA 0.472328 0.0016610 13537856 0.00000 NA NA 88.05 40936487 1.0394206 NA 50 100.00000 16.16385 50
hawkins ctrl_1 55732128 82244817 82244817 55732128 100 55732128 0.0001172 1.04 NA NA NA 0.402003 0.0022973 26512689 0.00000 NA NA 86.11 48794129 2.8396430 NA 49 100.00000 36.13990 49
hawkins ctrl_2 56249612 87079998 87079998 56249612 100 56249612 0.0001425 1.05 NA NA NA 0.446901 0.0022671 30830386 0.00000 NA NA 84.24 48318433 3.0143122 NA 50 100.00000 40.06617 50
hawkins fus_1 56937877 91180287 91180287 56937877 100 56937877 0.0000613 1.05 NA NA NA 0.434754 0.0023454 34242410 0.00000 NA NA 83.85 48671327 3.3447031 NA 50 100.00000 39.16021 50
hawkins fus_2 55697111 91222990 91222990 55697111 100 55697111 0.0000492 1.06 NA NA NA 0.473655 0.0023033 35525879 0.00000 NA NA 82.82 46919285 3.2152090 NA 51 100.00000 42.74376 50
lee.ALS spinal_c9orf72_1 176059847 295475531 295475531 176059847 100 176059847 0.0000603 1.04 0.00000 NA NA 0.583518 0.0028718 119415684 0.00000 NA NA 80.38 144676081 1.3170423 NA 48 75.49589 49.68399 48
lee.ALS spinal_c9orf72_2 158118940 248292842 248292842 158118940 100 158118940 0.0000524 1.05 0.00000 NA NA 0.625328 0.0026696 90173902 0.00000 NA NA 81.79 132037661 1.5092816 NA 48 75.49558 53.24453 48
lee.ALS spinal_c9orf72_3 165519831 397216894 397216894 165519831 100 165519831 0.0000592 1.06 0.00000 NA NA 0.682174 0.0029370 231697063 0.00000 NA NA 61.79 119197894 1.3272903 NA 51 75.49916 60.90015 51
lee.ALS spinal_ctrl_1 56334539 91703261 91703261 56334539 100 28153597 0.0000924 1.04 18.87285 NA NA 0.663619 0.0039929 35368722 99.95146 NA NA 79.50 23895796 NA NA NA NA NA NA
lee.ALS spinal_ctrl_2 67107456 106347097 106347097 67107456 100 33535748 0.0000420 1.04 17.48065 NA NA 0.696667 0.0041699 39239641 99.94641 NA NA 80.24 28822340 NA NA NA NA NA NA
lee.ALS spinal_ctrl_3 57737133 107257696 107257696 57737133 100 28847016 0.0004675 1.18 12.25616 NA NA 0.746278 0.0043442 49520563 99.92535 NA NA 74.28 23174968 NA NA NA NA NA NA
lee.ALS spinal_sod1_1 130130020 224968136 224968136 130130020 100 130130020 0.0000244 1.07 0.00000 NA NA 0.590068 0.0027903 94838116 0.00000 NA NA 80.01 106453731 0.6998293 NA 48 75.51113 50.05608 48
lee.ALS spinal_sod1_2 177533609 254297645 254297645 177533609 100 177533609 0.0000394 1.06 0.00000 NA NA 0.624196 0.0026957 76764036 0.00000 NA NA 84.00 151337173 1.5103653 NA 48 75.46761 53.56905 48
lee.ALS spinal_sod1_3 152556502 215300982 215300982 152556502 100 152556502 0.0000365 1.09 0.00000 NA NA 0.634475 0.0026854 62744480 0.00000 NA NA 83.98 130245147 1.7993886 NA 48 75.49433 54.11551 48

Fig 1 Pipeline schematic

PCA

ipsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
  mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS",  dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~  dataset), library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero"), #dataset = gsub("\\."," ",dataset), #dataset = str_to_title(dataset),
         DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~  DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
         ) %>%
  left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))

# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, shape = library_type)) + geom_point(aes(color=dataset), size=1) +
  scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
  theme_oz() + theme(legend.text=element_text(size=8), legend.title=element_text(size=7), legend.position = "right", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
  ggforce::geom_mark_ellipse(aes(label = library_type), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE) + guides(color=guide_legend(title="Dataset", keywidth=0.1, keyheight=0.15, default.unit="inch"))
ipsc_mn_als_datasets_with_lee.pca_dataset

Cell type marker heatmap

astrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB",  "FGFR3",  "SLC4A4", "DIO2")
endo.markers = c("CLDN5",  "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG",  "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")

undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")

nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")    
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#"NEFH",
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3") 
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>% 
  mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers", 
                           gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers", 
                           gene_name %in% mn.markers ~ "mn.markers"), 
         group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))

### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered

celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = celltype.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = celltype.markers.df.filt$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL, 
          show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6), 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),  labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmap

Fig S2-3 PCA

Fig S1 is the PRISMA flow diagram

PC1 & PC2 gene loadings

ipsc_mn_als_datasets_with_lee.vsd.rv <- rowVars(assay(ipsc_mn_als_datasets_with_lee.vsd)) # calculate the variance for each gene
ipsc_mn_als_datasets_with_lee.vsd.ntop_genes <- order(ipsc_mn_als_datasets_with_lee.vsd.rv, decreasing=TRUE)[seq_len(min(500, length(ipsc_mn_als_datasets_with_lee.vsd.rv)))] # select the ntop genes by variance
ipsc_mn_als_datasets_with_lee.vsd.pca <- prcomp(t(assay(ipsc_mn_als_datasets_with_lee.vsd)[ipsc_mn_als_datasets_with_lee.vsd.ntop_genes,])) # perform a PCA on the data in assay(x) for the selected genes
ipsc_mn_als_datasets_with_lee.vsd.loadings <- as_tibble(ipsc_mn_als_datasets_with_lee.vsd.pca$rotation, rownames = "gene_id") %>% left_join(gene2ens) %>% arrange(PC1) %>% select(gene_name, gene_id, everything())

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2")#,"ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
neuronal.markers = c(nonspecific.neuronal, dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain)

# scatter all PC1 vs PC2
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatter = ggplot(ipsc_mn_als_datasets_with_lee.vsd.loadings, aes(x = PC1, y = PC2 )) + 
    labs(x = "PC1 gene loading", y = "PC2 gene loading") +
    geom_hline(yintercept = 0, linetype = 3) + geom_vline(xintercept = 0, linetype = 3) +
    geom_point(size = 1, alpha = 0.1) +
    scale_fill_continuous(type = "viridis") +
    guides(fill = FALSE) +
    theme_oz() +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^H[1-9]",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^SNOR|RN7SK|RMRP|RPPH1",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
  geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings,  gene_name %in% c(neuronal.markers, HOX.markers)), aes(x = PC1, y = PC2, label = gene_name), colour = "black", size = 2.3) +
  annotate("text", x = 0.04, y = 0.05, label = "PC1+ PC2+",size = 3, color = "black") + annotate("text", x = -0.07, y = -0.12, label = "PC1- PC2-", size = 3, color = "firebrick2") + 
  annotate("text", x = 0.04, y = -0.12, label = "PC1+ PC2-", size = 3, color = "black") + annotate("text", x = -0.07, y = 0.05, label = "PC1- PC2+", size = 3, color = "black")
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatter

Sample characteristics

ipsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
  mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS",  dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~  dataset), 
         DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~  DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
         library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","mitchell","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero")) %>%
  left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))

# multiqc stats
multiqc_general_stats_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_general_stats_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), 
     # multiqc_general_stats_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_general_stats_stat_paths)
     ) %>% pull(multiqc_general_stats_stat_paths)
multiqc_general_stats.tsv = multiqc_general_stats_stat_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_general_stats.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_general_stats <- map_dfr(multiqc_general_stats.tsv, bind_rows, .id = "database_dir") %>% clean_names()
multiqc_rseqc_read_distribution_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_rseqc_read_distribution_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"),
     # multiqc_rseqc_read_distribution_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_rseqc_read_distribution_paths)
     ) %>% pull(multiqc_rseqc_read_distribution_paths)
multiqc_rseqc_read_distribution.tsv = multiqc_rseqc_read_distribution_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_rseqc_read_distribution.tsv) =  ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_rseqc_read_distribution <- map_dfr(multiqc_rseqc_read_distribution.tsv, bind_rows, .id = "database_dir") %>% clean_names()
ipsc_mn_als_datasets_with_lee.pcaData = ipsc_mn_als_datasets_with_lee.pcaData %>% left_join(multiqc_general_stats) %>% left_join(multiqc_rseqc_read_distribution) # need unique sample names - If multiple dataset names within a single multiqc_general_stats.txt then will only join the first dataset name

# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=dataset)) + geom_point(size=1) +
  scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
  theme_oz() + theme(legend.position = "none") + guides(color=guide_legend(keywidth=0.5, keyheight=0.5, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
  ggforce::geom_mark_ellipse(aes(label = dataset), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE)
ipsc_mn_als_datasets_with_lee.pca_dataset

# Colour by library_type
ipsc_mn_als_datasets_with_lee.pca_library_type <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=library_type)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))+labs(colour="Library preparation")
ipsc_mn_als_datasets_with_lee.pca_library_type

# Colour by instrument
ipsc_mn_als_datasets_with_lee.pca_instrument <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=instrument)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_blank(), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_instrument

# Colour by DIV
ipsc_mn_als_datasets_with_lee.pca_DIV <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=DIV)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top"))  + labs(color="Days in vitro") + 
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_DIV

# Colour by ALS
ipsc_mn_als_datasets_with_lee.pca_als <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=condition)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_als

# Colour by mutation
ipsc_mn_als_datasets_with_lee.pca_mutation <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=mutation)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_mutation

# Colour by gender
ipsc_mn_als_datasets_with_lee.pca_gender <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=gender)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) 
ipsc_mn_als_datasets_with_lee.pca_gender

RNAseq QC metrics

Fig S3

# Colour by strandedness
ipsc_mn_als_datasets_with_lee.pca_strandedness <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=strandedness)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.2, keyheight=0.2, default.unit="inch")) + 
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_strandedness

# Colour by read depth
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_raw_total_sequences)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6, angle = 0), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(1, 'cm'))  + 
  guides(color = guide_colourbar(title = "read depth", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_raw_total_sequences,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences

# Color by intronic read % intron_read_pct
ipsc_mn_als_datasets_with_lee.pca_read_distribution <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=introns_tag_pct)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "intronic reads %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$introns_tag_pct,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) 
ipsc_mn_als_datasets_with_lee.pca_read_distribution

# Colour by biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "ribosomal rna %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna

# Colour by quali_map_mqc_generalstats_qualimap_5_3_bias
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_5_3_bias)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "5' 3' bias", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=1, low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias

# Colour by quali_map_mqc_generalstats_qualimap_reads_aligned
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_reads_aligned)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Reads aligned", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$quali_map_mqc_generalstats_qualimap_reads_aligned,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned

# Colour by picard_mqc_generalstats_picard_percent_duplication
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=picard_mqc_generalstats_picard_percent_duplication)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Read duplication %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$picard_mqc_generalstats_picard_percent_duplication,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +  
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication

# Colour by samtools_mqc_generalstats_samtools_reads_mapped
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_reads_mapped)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
  guides(color = guide_colourbar(title = "Reads mapped", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_reads_mapped,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped

# Colour by star_mqc_generalstats_star_uniquely_mapped_percent
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percent <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=star_mqc_generalstats_star_uniquely_mapped_percent)) + geom_point(size=1) + 
  theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) + 
  guides(color = guide_colourbar(title = "Reads uniquely mapped %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top"))  + 
  scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$star_mqc_generalstats_star_uniquely_mapped_percent,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
  xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) +  ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percent

Fig S4-9 Heatmap expression

Cell type marker heatmap

astrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB",  "FGFR3",  "SLC4A4", "DIO2")
endo.markers = c("CLDN5",  "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG",  "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")

undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")

nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")    
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") 
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3") 
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>% 
  mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers", 
                           gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers", 
                           gene_name %in% mn.markers ~ "mn.markers"), 
         group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))

### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered

celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = celltype.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = celltype.markers.df.filt$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL, 
          show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6), 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),  labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmap

Neuron type markers

nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#,"NEFH"
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3","ETV1", "NOS1","RUNX1","NOTCH1","ARHGAP36","SLC10A4","POU3F1","FOXP2","ISL2") #
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")#dl.domains LDB1 "LHX1","POU4F1",,"LBX1""LHX2","LHX9","DRGX","LMX1B","VSX2","EVX2","LMO4"
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)

neuron.type.markers = c(motor.neuron.progenitor, postmitotic.motor.neuron, nonspecific.neuronal,interneuron.markers) 
neuron.type.markers.df = tibble("gene_name" = neuron.type.markers) %>% filter(gene_name %in% neuron.type.markers) %>% 
  mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% motor.neuron.progenitor ~ "motor.neuron.progenitor", 
                           gene_name %in% postmitotic.motor.neuron ~ "postmitotic.motor.neuron", #gene_name %in% oculomotor.markers ~ "oculomotor.markers", 
                           gene_name %in% interneuron.markers ~ "interneuron"), 
         group = factor(group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuron.type.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% neuron.type.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = neuron.type.markers.df$gene_name)) %>% select(-gene_id) %>% 
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
neuron.type.markers.df.filt = neuron.type.markers.df %>% filter(gene_name %in% neuron.type.markers.marker$gene_name)
neuron.type.markers.marker.mat <- make_matrix(select(neuron.type.markers.marker,-gene_name), pull(neuron.type.markers.marker,gene_name))

### Cluster samples ###
neuron.type.markers.rnaseq.heatmap <- Heatmap(t(neuron.type.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
          column_order = neuron.type.markers.df.filt$gene_name,
          column_names_gp = gpar(fontsize = 6), 
          column_split = factor(neuron.type.markers.df.filt$group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron")),
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",4)), labels = c("nonspecific\nneuronal", "motor neuron\nprogenitor", "postmitotic\nmotor neuron", "interneuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          column_title = NULL, 
          show_row_names = FALSE,
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
neuron.type.markers.rnaseq.heatmap

Dorso-ventral markers

Markers are from Fig 2 in https://journals.biologists.com/dev/article/148/15/dev199711/271192/Single-cell-transcriptome-profiling-of-the-human

nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")

neuronal.markers = c(dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain) #nonspecific.neuronal
neuronal.markers.df = tibble("gene_name" = neuronal.markers) %>% 
  mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% dl.domains ~ "dl.domains", 
                           gene_name %in% V0.domain ~ "V0.domain", gene_name %in% V1 ~ "V1", 
                           gene_name %in% V2a.domain ~ "V2a.domain", gene_name %in% V2b.domain ~ "V2b.domain", gene_name %in% MN.domain ~ "MN.domain", gene_name %in% V3.domain ~ "V3.domain"), 
         group = factor(group, levels = c("dl.domains","V0.domain", "V1", "V2a.domain", "V2b.domain", "MN.domain", "V3.domain"))) %>% 
  arrange(group) %>% distinct(gene_name, .keep_all = TRUE)

# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuronal.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% 
  filter(gene_name %in% neuronal.markers.df$gene_name) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst)))  %>% 
  arrange(factor(gene_name, levels = neuronal.markers.df$gene_name)) %>% select(-gene_id) %>%
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% select(-contains("answerals_CASE"))
neuronal.markers.marker.mat <- make_matrix(select(neuronal.markers.marker,-gene_name), pull(neuronal.markers.marker,gene_name))

### Cluster samples ###
neuronal.markers.marker.centered_mat = t(scale(t(neuronal.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
dorsoventral.markers.heatmap <- Heatmap(t(neuronal.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
          column_order = neuronal.markers.df$gene_name,
          column_names_gp = gpar(fontsize = 7), 
          column_split = neuronal.markers.df$group,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",7)), labels =  c("dl\ndomains","V0\ndomain", "V1", "V2a\ndomain", "V2b\ndomain", "MN\ndomain", "V3"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
          column_title = NULL, column_title_gp = gpar(fontsize = 8), 
          cluster_columns = FALSE, cluster_column_slices = FALSE, 
          cluster_rows = FALSE,
          row_title = NULL, 
          row_split = dataset.samples.df$dataset,
          show_row_names = FALSE, 
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)))
dorsoventral.markers.heatmap

Rostro-caudal markers

HOX markers

HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
HOX.markers.df <- data.frame(row.names = HOX.markers, gene_name = HOX.markers) %>% 
  mutate(group = gsub("HOX[A-D]","", gene_name), group = factor(as.numeric(gsub("-AS$","", group)))) %>% 
  arrange(group) %>% 
  mutate(level = factor(case_when(group %in% c(1,2,3) ~ "Hindbrain", group %in% c(4,5,6,7) ~ "Cervical", group %in% c(8,9) ~ "Thoracic", 
                                  group %in% c(10,11) ~ "Lumbar", TRUE ~ "Sacral"), levels = c("Hindbrain","Cervical","Thoracic","Lumbar","Sacral")))
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
HOX.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% distinct(gene_name, .keep_all = TRUE) %>% 
  filter(gene_name %in% HOX.markers.df$gene_name) %>% 
  dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>% 
  arrange(factor(gene_name, levels = HOX.markers.df$gene_name)) %>% select(-gene_id) %>%
  rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% 
  select(-contains("answerals_CASE"))
HOX.markers.marker.mat <- make_matrix(select(HOX.markers.marker,-gene_name), pull(HOX.markers.marker,gene_name))
HOX.markers.marker.centered.mat = t(scale(t(HOX.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
HOX.markers.heatmap <- Heatmap(t(HOX.markers.marker.mat), 
          border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
          column_order = HOX.markers.df$gene_name,
          column_names_gp = gpar(fontsize = 7), 
          column_split = HOX.markers.df$level,
          bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Hindbrain", "Cervical", "Thoracic","Lumbar","Sacral"), labels_gp = gpar(fontsize = 8), labels_rot = 0)),
          column_title = NULL, column_title_gp = gpar(fontsize = 8), 
          cluster_columns = FALSE, cluster_column_slices = FALSE, 
          cluster_rows = FALSE,
          row_title = NULL, 
          # row_order = dataset.samples.df$dataset_sample,
          row_split = dataset.samples.df$dataset,
          show_row_names = FALSE, 
          right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",17)), 
                                                                 labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"), 
                                                                 labels_gp = gpar(fontsize = 7), labels_rot = 0)))
HOX.markers.heatmap